When you add derivatives like sulfates you need to adjust the charge on the connecting oxygen. See here: http://legacy.glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/
This is already done for you by the website, however the charge information gets lost when you take just the pdb file and load it into tleap. Instead you could build your 3D structure on the website and click "Download All". Then look for either structure.off (if you want the unminimized version) and do this in tleap: loadoff structure.off ## The term CONDENSEDSEQUENCE is defined in the file structure.off check CONDENSEDSEQUENCE saveamberparm CONDENSEDSEQUENCE unminimized-gas.parm7 unminimized-gas.rst7 etc
*Repeating units* We have an upcoming polybuilder in testing that will allow you to build repeating units on Glycam-Web. For now you can create your own in the build-via-text tool (glycam.org/txt). It's often much faster to use this if you have multiple large sequences with small edits.
Some examples are: [4DManpa1-]<5>OME With a "head" and "tail": DGalpa1-4[4DManpa1-]<5>3DGlcpa1-OME [4LIdopA[2S]a1-4DGlcpNS[6S]a1-]<5>OME Branches in repeating unit: DGlcpa1-4[4DGlcpa1-]<4>2DGlcpa1-4[4DGlcpa1-6[LFucpa1-2]DManpa1-]<2>OH Nested repeats: [4DGlcpa1-]<2>2DGulpa1-4[4DAllpa1-6[4DGalpa1-]<2>4DManpa1-]<2>3DManpa1-2[4DAllpa1-6[[4DGalpa1-]<3>4]DManpa1-]<3>OH
Hello everyone, I was trying to build a glycoprotein on GLYCAMM. I was able to construct all the necessary glcyans and also found the glycosylation sites to be active. However, when I download the file, there are no glycans on it and I only get the pdf files, I also need the prmtop and inpcrd files. I saw that another user had the same issue. Could you please help me in solving this! Best, Natesan.
It would help if you could share some more information about your project. Did you enter an email address? DId you get a notice that your project had completed? If not, do you mind doing that? If you can forward the email to me ([log in to unmask]), I will be better able to figure out what happened. Otherwise, if you assigned the project a name, tell me the name. Thanks!
Hello, Thanks for your reply. The email address I used is [log in to unmask] I currently have assigned a project which is running now, the name of the project is a2g0f_m5. Best, Natesan.
When you get the email saying that your project is complete, please forward it to [log in to unmask]
If you do not receive an email in 24 hours, let me know.
On Mon, Oct 30, 2023 at 9:48 AM Natesan Mani <[log in to unmask]> wrote: > > Hello, > Thanks for your reply. The email address I used is [log in to unmask] I currently have assigned a project which is running now, the name of the project is a2g0f_m5. > Best, > Natesan. > > ________________________________ > From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of Lachele Foley <[log in to unmask]> > Sent: Monday, October 30, 2023 3:09
The job just completed, and I forwarded the email to you. I also got this error when I submitted the job: "java.io.FileNotFoundException: /website/dev.glycam/userdata/tools/mdfiles/a2g0f_m5_172098d6-79e2-4f17-92ad-1f4ec755d624/stderr_file (No such file or directory)". I refreshed the page and the job was completed. Best, Natesan.
Thanks. We will check into this and get back to you.
On Mon, Oct 30, 2023 at 9:54 AM Natesan Mani <[log in to unmask]> wrote: > > The job just completed, and I forwarded the email to you. I also got this error when I submitted the job: "java.io.FileNotFoundException: /website/dev.glycam/userdata/tools/mdfiles/a2g0f_m5_172098d6-79e2-4f17-92ad-1f4ec755d624/stderr_file (No such file or directory)". I refreshed the page and the job was completed. > Best, > Natesan. > > ________________________________ > From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of Lachele Foley <[log in to unmask]> > Sent: Monday, October 30, 2023 9:50 AM > To: [log in to unmask] <[log in to unmask]> > Subject: Re: Regarding Glycoprotein builder
Hello, I did some testing from my end, and it seems like adding more than 5 glycans to my system is giving me the aforementioned error. I have a total of 7 glycans in my system. The glycoprotein builder works perfectly when there are 5 glycans added but adding more than 5 is giving me the error. I am not sure if glycam has a limit on how many glycans can be added. Please let me know !
There is no limit, but if the overall system size becomes too large, there might be trouble.
Several of us have varying obligations this week, so we can't be fast, but we are looking into the issue.
You could try doing the first five and then the last two as separate jobs. Then, with some work, you could add the last two to the first system. This is possible because we do not alter the coordinate space of the protein significantly. You might need to manually rotate some bonds if there are clashes. Also, definitely check the orientation of the
Hello Glycam users, I am planning to do MD simulation of heparin sulfate. I build the structure(LIdopA[2S]a1-4DGlcpNS[6S]a1-4LIdopA[2S]a1-4DGlcpNS[6S]a1-OH) using GAG builder. I used GLYCAM_06j-1.prep and GlcNs_preliminary.prep files in tleap to generate topology and coordinate files, but when loading the pdb file obtained from GAG builder in tleap, I am getting the following error. Error: Comparing atoms .R<SO3 3>.A<O1 2>, .R<UYS 2>.A<O4 24>, .R<SO3 3>.A<O2 3>, and .R<SO3 3>.A<O3 4> to atoms .R<SO3 3>.A<O1 2>, .R<YuA 1>.A<C1 1>, .R<SO3 3>.A<O2 3>, and .R<UYS 2>.A<O4 24> This error may be due to faulty Connection atoms. !FATAL ERROR---------------------------------------- !FATAL: In file [chirality.c], line 142
Glycam-web now gives you a mol2 file called min-gas.mol2. It contains charges, atom types and connectivity, so you can just load that into tleap instead of the pdb file and avoid the below:
What you see is from an issue with automatic atom connectivity in tleap; it assumes each residue is connected to the previous residue via the head and tail atoms and so creates bonds automatically. Works great for linear molecules like proteins. For branched carbohydrates (the sulfates are considered branches as they are separate residues) you need to add TER cards between residues that should not
I am working on a pdb file called 1gmo in tleap, it contains proteins and glycans and I am facing some issues while working with the glycan part. I loaded GLYCAM_06j-1 force field but the glycans (IDS and SGN) are not getting recognized. I am getting errors saying Unknown residue and the glycans does not have a type.
I faced the same problem some time ago. I found that you need to download additional parameters from the glycam web page. If you go into https://glycam.org/docs/forcefield/all-parameters/index.html you will see that there are several files in the Special Releases section. You should download one Parameter File (frcmod.UnsaturatedRing-ProtonatedUA) and four Prep Files (GlcNS_prep_files, GlcNH2_and_GlcHN3, 4,5Unsaturated_and_Protonated_UA and 4DGlcpNH3+b) and load them all in tleap, with the loadAmberPrep and loadamberparams commands, before loading your structure. Hope it works.
Thanks for the reply, the files you mentioned have no download option. When I click the files, their content opens in a new window in a text format and no download option appears from where I can get these files in a proper format.
Should I just copy and paste the content of these files as such or any proper format is required ?
You should save them as plain text. If you click on them in Firefox, for instance, a new window will be open with all the contents of the file but without proper format:
MASS BOND C -Ck 214.0 1.466 * Average (1.494) from CSD structures HEMKEP,KORCOJ,SRHXGU,MIZFUX,GUVFOs,GUVFEI, & GUVFAE C -Cj 214.0 1.466 * Duplicate of C -Ck C -Oh 450.0 1.364 PARM99 - JCC,7,(1986),230; (not used any more for TYR) ANGL H1-Cg-N3 50.0 109.5 * G06 - MT for NH3+, copy of HP-CT-N3 Ck-C -O2 49.5 113.4 * Average (117.9) from CSD structures HEMKEP,KORCOJ,SRHXGU,MIZFUX,GUVFOs,GUVFEI, & GUVFAE C -Ck-Ck
I guess the problem is the naming of residues. In your 1GMO pdb file all the glucosamine residues are label as SGN and all iduronic as IDS. Glycam has different ways of naming these, depending on what is their state. You have to take a look to the files Docs_Glucosamine and Docs_uronic_acids, which you will find in the same page where you found the special parameters, and name the SGN/IDS residues according to them. You can also take a look at https://glycam.org/docs/forcefield/glycam-naming-2/index.html. There are also some issues that you have to take into account with sulphated residues (https://glycam.org/docs/help/2014/04/04/sulfating-glycam-residues/index.html)
The leap will not recognize IDS and SGN (if there have not been any recent developments I am unaware of), as these residue names are not used in Glycam FF. You can have a look at this page to see how the glycan residue names should be renamed: https://glycam.org/docs/forcefield/glycam-naming-2/index.html
It looks complicated at first but is not so difficult. Alternatively, you can build the same glycan in Glycam-web GAG builder and see which residue number should be renamed to what.
Thank you for the suggestions. I tried Charmm-GUI and yes there is a problem of chemically modified glycans. I will try to use the alternatives that you have mentioned.
I am trying to solvate a glycoprotein-protein complex with tleap, and upon attempting I get this error below. I’ve checked the connections between the atoms in the glycan and can’t find any obvious problems. Maybe it’s due to VMA being assigned as residue 1 for some reason, as it should be residue 502 (relevant section of pdf file also included below)? Any help would be appreciated.
Not sure though but it looks like a branched N-glycan. In that case, you might have to put a TER in between the residues (at lest 500 and 501 based on the error) and use the bond command tleap to create bonds. I can look into this if you provide both your complete PDB file and the tleap script.
I'm trying to build a simple heparin disaccharide using the GAG-builder on GLYCAM (not legacy) for MD simulations - UA2S-4,5 -->GlcNS6S-OH - but it throws an error:
*There was a problem making the default sequence request: The deduced linkageLabel is too small: A-4. We require anomer, start atom number, a dash, and connecting atom number. Example: a1-4*
It's a known bug with dUA, fixed already on test: test.glycam.org/url/condensed/dUAa1-4DGalpNAc[6S]b1-OME
Best, Oliver Grant Research Scientist - Woods Lab Complex Carbohydrate Research Center University of Georgia
On Mon, Oct 24, 2022 at 4:32 PM Samuel Holmes <[log in to unmask]> wrote:
> Hey Oliver, > > I'm trying to build a simple heparin disaccharide using the GAG-builder on > GLYCAM (not legacy) for MD simulations - UA2S-4,5 -->GlcNS6S-OH - but it > throws an error: > > *There was a problem making the default sequence request: The deduced > linkageLabel is too small: A-4. We require anomer, start atom number, a
I wouldn't say it's fixed. It stays stuck in minimization.
Sam
On Mon, Oct 24, 2022 at 1:17 PM Oliver Grant <[log in to unmask]> wrote:
> Hi Sam, > > It's a known bug with dUA, fixed already on test: > test.glycam.org/url/condensed/dUAa1-4DGalpNAc[6S]b1-OME > <http://test.glycam.org/url/condensed/dUAa1-4DGalpNAc%5B6S%5Db1-OME> > > Best, > Oliver Grant > Research Scientist - Woods Lab > Complex Carbohydrate Research Center > University of Georgia > > > On Mon, Oct 24, 2022 at 4:32 PM Samuel Holmes <[log in to unmask]> wrote: > >> Hey Oliver, >> >> I'm trying to build a simple heparin disaccharide using the GAG-builder >> on GLYCAM (not
Yes you're right, anything that contains dUA gets stuck in minimization, while other structures finish. We'll dig into it and get back to you.
Best,
Oliver Grant Research Scientist - Woods Lab Complex Carbohydrate Research Center University of Georgia
On Mon, Oct 24, 2022 at 9:39 PM Samuel Holmes <[log in to unmask]> wrote:
> Oliver, > > I wouldn't say it's fixed. It stays stuck in minimization. > > Sam > > On Mon, Oct 24, 2022 at 1:17 PM Oliver Grant <[log in to unmask]> > wrote: > >> Hi Sam, >> >> It's a known bug with dUA, fixed already on
On Tue, Oct 25, 2022, 3:08 AM Oliver Grant <[log in to unmask]> wrote:
> Hi Sam, > > Yes you're right, anything that contains dUA gets stuck in minimization, > while other structures finish. We'll dig into it and get back to you. > > Best, > > Oliver Grant > Research Scientist - Woods Lab > Complex Carbohydrate Research Center > University of Georgia > > > On Mon, Oct 24, 2022 at 9:39 PM Samuel Holmes <[log in to unmask]> wrote: > >> Oliver, >> >> I wouldn't say it's fixed. It stays stuck in minimization. >>
I noticed that legacy is back up, which is great. The legacy site can handle UA-4,5 residues. However, once I try to parametrize it in LEAP, GLYCAM-06j does not seem to have a prep file for that residue, which I believe the code is 245? Do you have that prep file you could send me?
On Thu, Nov 10, 2022 at 12:57 PM Samuel Holmes <[log in to unmask]> wrote:
> Hey Oliver, > > I noticed that legacy is back up, which is great. The legacy site can > handle UA-4,5 residues. However, once I try to parametrize it in LEAP, > GLYCAM-06j does not seem to have a prep file for that residue, which I > believe the code is 245? Do you have that prep file you could send me? > > Thanks, > > Sam > > On Tue, Oct 25, 2022 at 9:09 AM Samuel Holmes <[log in to unmask]> wrote:
On Thu, 10 Nov 2022 at 18:59, Samuel Holmes <[log in to unmask]> wrote:
> Specifically the 2-O-sulfated one. > > Sam > > On Thu, Nov 10, 2022 at 12:57 PM Samuel Holmes <[log in to unmask]> wrote: > >> Hey Oliver, >> >> I noticed that legacy is back up, which is great. The legacy site can >> handle UA-4,5 residues. However, once I try to parametrize it in LEAP, >> GLYCAM-06j does not seem to have a prep file for that residue, which I >> believe the code is 245? Do you have that prep file you could
Going off of the filenames and where I have them stored, I believe these are what the legacy website uses to generate the 3D structures you get on there.
Best,
Oliver Grant Research Scientist - Woods Lab Complex Carbohydrate Research Center University of Georgia
On Thu, Jul 21, 2022 at 5:36 PM Samuel Holmes <[log in to unmask]> wrote:
> Hey there Oliver/Lachele, > > Could you possibly send me the prep files for the 4 letter code residues > representing the different puckers of IdoA (4C1, 1C4, 2SO)? > > I'm trying to get some practice with building HS oligosaccharides
On Fri, Jul 22, 2022 at 5:54 AM Oliver Grant <[log in to unmask]> wrote:
> Hi Sam, > > Going off of the filenames and where I have them stored, I believe these > are what the legacy website uses to generate the 3D structures you get on > there. > > Best, > > Oliver Grant > Research Scientist - Woods Lab > Complex Carbohydrate Research Center > University of Georgia > > > On Thu, Jul 21, 2022 at 5:36 PM Samuel Holmes <[log in to unmask]> wrote: > >> Hey there Oliver/Lachele, >> >> Could you
Sorry to annoy you again, but I also need the prep files for the 2-O-sulfated versions of the different IdoA puckers. Or I could maybe edit the prep files you gave me and make an open valence at the C2 oxygen?
Thanks,
Sam
On Sun, Jul 24, 2022 at 11:14 AM Samuel Holmes <[log in to unmask]> wrote:
I think the prep file you sent me for IdoA(2SO) is incorrect. It has two oxygens linked to each other at C4 where there should be an open valence.
Sam
On Sun, Jul 24, 2022 at 11:41 AM Samuel Holmes <[log in to unmask]> wrote:
> Oliver, > > Sorry to annoy you again, but I also need the prep files for the > 2-O-sulfated versions of the different IdoA puckers. Or I could maybe edit > the prep files you gave me and make an open valence at the C2 oxygen? > > Thanks, > > Sam > > On Sun,
Adding derivatives like sulfates is do-able in tleap, but a bit tricky ( https://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/index.html). The website does this on the fly.
Can you send your leap input files so I can reproduce the issue with IdoA(2SO). I don't see anything from eyeballing the prep file.
Best,
Oliver Grant Research Scientist - Woods Lab Complex Carbohydrate Research Center University of Georgia
I have been using GAG builder. Is there a way to directly read pdb file (GAGs), assign the Glycam force field and convert it to AMBER?
Thank you for kind attention.
Regards, Neha
Dr. Neha S. Gandhi | Advance Queensland Senior Research Fellow School of Chemistry and Physics| Personalised Therapies (Program leader), Science and Engineering Faculty | Queensland University of Technology M-O-Block, Gardens Point Campus ph 3138 7394| email: [log in to unmask]<mailto:[log in to unmask]> CRICOS No 00213J
Note that the legacy website is down so you won't have access to the gag builder right now, but if you take the sequence you generate there and paste it into the carb builder on glycam.org/txt you can generate the gag there and it gives you an off file when you download all from the rightmost column of the download page. You can directly load that off file into tleap using:
From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> On Behalf Of Oliver Grant Sent: Monday, 18 July 2022 11:52 PM To: [log in to unmask] Subject: Re: Reading GAG pdb files and converting to amber
Hi Neha,
Note that the legacy website is down so you won't have access to the gag builder right now, but if you take the sequence you generate there and paste it into the carb builder on glycam.org/txt you can generate the gag there and it gives you an off file when you download all from the rightmost column of the download page. You can directly load
1. After I built the glycoprotein, I read it using amber-tleap, and its charge was not an integer after loading the force field, which made the tleap report a warning. Here's the force field I use： source leaprc.GLYCAM_06j-1 source leaprc.protein.ff19SB source leaprc.water.tip3p loadamberparams frcmod.ionsjc_tip3p
Can you send the files you are loading into tleap? It sounds from the charge that the ROH is still there. Did you build the glycan only on glycam.org and you plan to attach it somehow or did you use the glycoprotein builder (glycam.org/gp)?
Best, Oliver Grant Research Scientist - Woods Lab Complex Carbohydrate Research Center University of Georgia
Thanks for the reply! I will send my PDB files, leap.log, .inpcrd and .prmtop, I used the glycoprotein builder (glycam.org/gp). Thanking you in advance
For some reason your ASN 11 where you attach the glycan is not being renamed to NLN, and so you'll have to manually do that before loading it into tleap. Do be careful when you load a branched glycan in, tleap will automatically bond residues in series as it reads them from the PDB file, so you need a TER card at branch points and an explicit bond command e.g: mol = loadpdb glyRBD.pdb bond mol.2.O6 mol.15.C1 That's just an example, you'll have to figure out the correct residue/atom numbers for your system. Check the prmtop and inpcrd
After I changed the residue name and the naming of the LINk in the pdb file from ASN to NLN, the charge after reading is no problem, the TER card is generated automatically from glycam.gb and it works fine so far. Thank you very much for answering and solving my problem from your busy schedule, and thank you most sincerely.
I'm trying to solvate and add counterions to a HS hexasaccharide in tLEAP. I have built the hexasaccharide using the GLYCAM web server, but once I load the PDB into LEAP, it does not recognize the UYS (GlcNS residue). I know that you released a prep file for GlcNS residues, and I downloaded that and tried loading that in as well, and got the same issue. Did I not format the prep file correctly or am I missing something more?
Prep files are weird, can you send the actual file you loaded into tleap with the command you used? Depending on e.g. how many emptry lines you put at the top of the file it might fail to load anything.
Best, Oliver
On Wed, 1 Jun 2022 at 17:48, Samuel Holmes <[log in to unmask]> wrote:
> Hey There GLYCAM, > > I'm trying to solvate and add counterions to a HS hexasaccharide in tLEAP. > I have built the hexasaccharide using the GLYCAM web server, but once I > load the PDB into LEAP, it does not recognize the UYS
Thanks for the speedy response! Sure thing, here is the prep file for the UYS residue, and the PDB of the hexasaccharide I was trying to solvate.
Sam
On Wed, Jun 1, 2022 at 12:56 PM Oliver Grant <[log in to unmask]> wrote:
> Hi Sam, > > Prep files are weird, can you send the actual file you loaded into tleap > with the command you used? Depending on e.g. how many emptry lines you put > at the top of the file it might fail to load anything. > > Best, > Oliver > > On Wed, 1 Jun
You needed four blank lines at the top of the prep file. That worked for me. Or you can load in all of the GlcNS parameters via the attached file.
Now you have other issues though: ERROR: The unperturbed charge of the unit: -9.093000 is not integral.
The write to the PDB file loses both connectivity and the charge adjustments we make after adding the sulfates. To load it into tleap from the pdb file and get the correct charges you'll now have to adjust the charges on the linking oxygen as per here: http://legacy.glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/index.html And you'll have
On Wed, Jun 1, 2022 at 2:31 PM Oliver Grant <[log in to unmask]> wrote:
> Hi Sam, > > You needed four blank lines at the top of the prep file. That worked for > me. Or you can load in all of the GlcNS parameters via the attached file. > > Now you have other issues though: > ERROR: The unperturbed charge of the unit: -9.093000 is not integral. > > The write to the PDB file loses both connectivity and the charge > adjustments we make after adding the
Hope your weekend was good. I've taken your instructions and have made some significant progress in LEAP, but I'm still left with a few warning messages about missing bond and bond angle parameters. Also, it doesn't appear that I have to do anything with the LINK cards, as the structure looks good in xLEAP when I use the "edit" command (but maybe that is not true, you tell me).
This is strange: No bond parameter for: - S No bond parameter for: Cg - Can't find angle parameter: -S-O2 Can't find angle parameter: H1 - Cg - Can't find angle parameter: Cg - - S Can't find angle parameter: Cg - Cg -
It looks like one of the atoms doesn't have a type, or it's type is an empty string somehow. Can you do this in tleap and send that along so I can try it locally? Even if the charge adjustments aren't made that's fine. You can do desc mol.2.C2 and see what it says.
Still getting the: Loading Prep file: ./UYS.prep ** LOOP atom C1 not found - bond not formed Discarding residue (-0.1940 ) to EOF when I load into tleap, and the file I downloaded was missing the 4 blank spaces at the beginning. There are funky things with windows vs linux endlines, so maybe that's the issue. You can use the GlcNS_preliminary.prep I sent previously or make sure there are four blank lines at the start of the file when you load it into leap. I was able to get a structure from what you sent using tleap, here's
Your prep file works. Maybe it's because in my prep file, I isolated only the prep file for UYS and don't have the prep files for the other GLYCAM residues? That might be why I was getting those weird warning messages. Anyways, I followed your instructions and it worked perfectly! Sometimes I just need to see exactly what someone is typing in the terminal for it to really stick. Thanks so much. I now need to attempt to add Ca2+ instead of Na+ counterions, but I think I can tackle that myself. I'll let you know if I'm struggling
Glad it's working. I was able to get your prep file working, I just needed to add the four blank lines at the top. I'm not planning to attend the gordon conference, but it looks like an interesting line-up. Enjoy!
I built a sulphated cellobiose using the new version of glycam tools. The linkage is beta 1-4 and the terminal is OMe.
When using the mol2 file or .off file, I have no issues building amber files from them. However, when I try using structure.pdb or min-gas.pdb file in tleap, I get following error Loading PDB file: ./min-gas.pdb
tleap is messing up the bonding. I can't be specific without seeing your pdb file, but when tleap reads pdb files it will automatically bond each residue to the previous residue. Works great for amino acids, but not branched molecules. You need to add a TER card, literally a line in the pdb file between the residues that just says TER like that, and tleap will not automatically bond those residues. However with branched structures you do need to specify where to actually bond. If you've loaded in your pdb file like this:
Thank you for your prompt response. I have seen similar queries on Glycam mailing list.
When I use the old version of Glycam tools, all sulfates are placed towards the end of the file. With the newer version of the tools, the sulfates are placed after each sugar (e.g. sugar backbone-sulfates-sugar backbone sulfate) and hence tleap shoots an error about the bonding. I am attaching both versions of pdb file and you will see what I mean.
Indeed, the “TER” are missing in the pdb files from the new glycam tools.
From: Neha S. Gandhi Sent: Wednesday, 9 March 2022 7:33 PM To: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> Subject: RE: new version- pdb files
Hi Oliver,
Thank you for your prompt response. I have seen similar queries on Glycam mailing list.
When I use the old version of Glycam tools, all sulfates are placed towards the end of the file. With the newer version of the tools, the sulfates are placed after each sugar (e.g. sugar backbone-sulfates-sugar backbone sulfate) and hence tleap shoots an error about
Thanks Neha, yes I see the issue. I'll fix this, but it will take some time for the fix to be propagated to the main website. I'll leave a note and write here again when it's done.
Best, Oliver Grant Research Scientist - Woods Lab Complex Carbohydrate Research Center University of Georgia
On Wed, Mar 9, 2022 at 10:33 AM Neha S. Gandhi <[log in to unmask]> wrote:
The fix is still underway as part of some larger changes. Note that even with the correct TER card placement for the sulfates, you'll still have to adjust charges on the connecting atom according to this: https://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/index.html
The website does this for you, but when it writes a pdb file the charges are lost. As you say it might be easier to work within mol2 format where the connectivity and charges are preserved. I haven't fully tested, but it looks like UCSF Chimera can successfully read and write from our mol2 (stick with the default settings though, selecting
Sorry I didn't reply to this as I wasn't sure. Perhaps someone else will chime in. As you say I don't think tleap will read that 4 letter sequence from a pdb file. You could load the frcmod and prep files into tleap and generate the 3D structure in there, rather than from a pdb file. There are instructions on how to do that in the amber manual: https://ambermd.org/doc12/Amber21.pdf Look for this line: glycan = sequence { ROH 6LB 6MB 0GA }
Thank you for your reply, I needed the protonated acid structure to implement it into the hyaluronan disaccharide and I have already succeeded in building the one where glucuronic acid is the terminal residue (I used the prep file Gla_2.prep). However, I am still not able to create the one where the acid is non-terminal. I‘ve noticed Monia Kam had a similar problem here three years ago, but the prep file mentioned there (Gla_1.prep) did not help me. There are additional faulty bonds present between the atoms O3-O5 and H3O-O5, I tried to modify the prep file, changing
If you want Protonated β-D-Glucuronic acid then you need 0ZBP, not 45B. I've copied the prep entry from the supplemental of https://pubmed.ncbi.nlm.nih.gov/28603292/ below, but this is indeed only the terminal version. If you want the 4-linked version I imagine you'll have to make it yourself. I'm not sure why this wasn't generated and released with the paper. Here are the steps you can follow to adjust the prep entry below so you can add at the O4, " *Hydrogen removal should be done within tleap or xleap (or with similar knowledge of the file structure) and not by
I followed your advice and succeeded in creating the structure in tleap without errors. However, when I visualize it, the glucuronic acid ring is split into two parts. It looks just like when I tried to modify the topological types of atoms in the prep file previously.
The log file is: source leaprc.GLYCAM_06j-1 loadamberparams frcmod.A-NAc loadamberprep A-NAc.prep
I imagine something is funky with your prep files. If you want to figure it out then this https://ambermd.org/doc/prep.html will help. However, I just checked and the only issue with the steps I wrote above is the remove command which you've corrected to: remove m.2 m.2.H4O
You'll also need to load in the prep file I sent to have 0ZBP available. tleap can read the 4 letter code fine from prep files, it just truncates it when writing to a PDB file, and can't read it from a PDB file.
I have finally achieved the right structure. I kept the residue name be 45B to be able to make some changes in the PDB file and reload it back to tleap. The geometry of the system was not optimal, however, I modified the coordinates manually according to another geo-optimized file and the structure is all right now.
Ok great news then :) Yes it uses "idealized" angles and energy minimization should bring it to a better geometry.
Best,
Oliver Grant Research Scientist - Woods Lab Complex Carbohydrate Research Center University of Georgia
On Thu, Mar 10, 2022 at 10:05 PM Pavlína Slavníková <[log in to unmask]> wrote:
> Hi Oliver, > > I have finally achieved the right structure. I kept the residue name be > 45B to be able to make some changes in the PDB file and reload it back to > tleap. The geometry of the system was not optimal, however, I modified the >
Hi we glycosylated the RBD in native sites but there is a problem with finding a bond OH-Cg. may you please help us? the commands and the structure are attached below thank you very much
The non-integral charge is also a red flag. Here are some issues: Asn11 that is conjugated to a glycan should be renamed to GLYCAM's format ASN residue name becomes NLN (N linked Asn). Ser162 should be OLS (O linked serine)
That should clear up the charge and other warnings (I didn't take it through tleap though).
I would like to run a simulation of a glycoprotein using TIP5P water. In the AMBER 18 manual (the version I'm using) it states on page 44 that an additional set of parameters has been created to use with TIP5P (GLYCAM-06EP). Looking in the amber directory, GLYCAM-06EP appears to have been replaced by GLYCAM-06EPb. This is also the version from the parameter download page on glycam.org. Unfortunately, my system contains six 4YB residues (3 Man5 glycans) which are not in GLYCAM-06EPb.
I have been tasked with running MD simulations of a oligosaccharide consisting of a modified D-Rha4Ac 1-2 repeats. The problem is that modifications are needed to the 4Ac group generating a “non-standard” derivative which does not have parameters in the forcefield (glycam), on every repeat.
I thought that it should probably be possible to combining GAFF or AMBER (ff14SB) with GLYCAM as seems to be basically what is happening when generating a glycoprotein. Especially as all atoms in the modified substituent are standard atoms and bonds (N,C,O,H).
No need for GAFF in this case. There are parameters for D-Rha and there is a residue "ACX" for Acetyl groups. The problem is that our carbohydrate builder (glycam.org/cb) doesn't allow you change from L to D for Rha (not sure why, but it's more common to need L-Rha as that's the natural one.). You can normally add the Acetyl group via our builder, but as the D form isn't available via our webtool it's not possible in this case. The glycam condensed sequence is for example DRhap[4A]a1-OH. It does look like our new builder on dev.glycam.org/cb would
Hello Oliver and thank you for a really nice and detailed reply!
I did play around a bit with this and was able to get the 4A group attached, roughly as you outlined.
My problem is that I need, amongst other things, an 4N”X" group instead of 4A. To avoid confusion, I would need a to replace the ether oxygen in the ester with a nitrogen, I think the correct terminology is “N-linked” though I am not sure. I would also need to modify the methyl part using different “unnatural” substituents.
Ok clearer now. Yes you could use GAFF for the varying part, but you do get into questions about how accurate you need it to be, and whether it's possible/reasonable to develop your own parameters. That's up to you to decide. I've mixed before, but I didn't need the end result to be very accurate. Mixing means creating your own frcmod for defining torsions, angles and bonds with the mixed atom types. You build the derivative prep file using GAFF atom type. Once you bond it in tleap it will tell you exactly what bonds, angles and torsion
At this point in time I can a level of tradeoffs regarding accuracy is acceptable. If initial investigations are interesting enough, this may need to be addressed at a later point in time.
So I think i have the general outline clear, I’ll get the prep/frcmod file for the derivative, build the “combined” structure” and have LEaP tell me what is missing, providing these details in a/the frcmod file. Along the lines of http://ambermd.org/tutorials/advanced/tutorial1/index.php.
So this little manoeuvre turned out to be “non-trivial”
I tried a whole set of different things, with different level of problems. Finally, I took antechamber generated gaff2 parameters and structure for the N-formyl group and aligned it with DRhapa1-OH in chimera, deleted the 4OH as well as one of the NH hydrogens, saved PDBs, merged into one PDB and here I run unto issues. This produced the least amount of errors/problems so far.
I'm not familiar with Antechamber. You'll need to make your own prep/lib file for the Rha with the N4. You can't use the Glycam one because it will indeed add in an O4. You'll also need a prep/lib file for each "derivative". The residue and atom names in the PDB file should match those in the prep/lib files. Use the bond command in tleap to bond the N4 to whatever atom in the derivative. Use the charge command in tleap to check the charge. It should be integral if you've done everything correctly.
That sounds reasonable, I had a feeling I missed a step somewhere and indeed it seems that I did. I have not performed a task like this in a very long time.
I’ll use glycam and the obtained structure to prepare the “intermediate” and accompanying lib/prep file in leap. A similar procedure for the substituent. Key difference will be to load the structure to be bonded with lib/prep/frcmod files instead of sourcing the FFs. Pretty sure I’ll manage to mess something up along the way though this feels like a good place to start.
So, I prepared a single DRhapa1-OH from glycam, loaded in leap, removed the 4-OH group and saved PDB and OFF file. I prepared the DRha[4NFo]pa1-OH with GAFF2 parameters. Loaded in leap, deleted everything but the "NFo” part, saved PDB and OFF part.
I prepared a single PDB with both both “fragments” hoping to load this with each OFF file in leap, then bonding them together using “bond” and checking for the missing parameters.
Can you send your inputs, scripts and outputs? I haven't tried this with lib files, but they should contain everything you need. Perhaps leap isn't capable of doing this.
Best, Oliver Grant Research Scientist - Woods Lab Complex Carbohydrate Research Center University of Georgia
On Wed, May 26, 2021 at 2:37 PM Gustaf Olsson <[log in to unmask]> wrote:
> Still missing the mark… > > So, I prepared a single DRhapa1-OH from glycam, loaded in leap, removed > the 4-OH group and saved PDB and OFF file. I prepared the DRha[4NFo]pa1-OH > with GAFF2 parameters. Loaded in leap, deleted everything
I took a chance and think I sent an archive and some ramblings to you email, of list.
Let me know if you prefer me posting the material here instead.
Best regards // Gustaf
On 27 May 2021, at 10:05, Oliver Grant <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi Gustaf,
Can you send your inputs, scripts and outputs? I haven't tried this with lib files, but they should contain everything you need. Perhaps leap isn't capable of doing this.
We have reports of persons submitting questions to this list, but that their questions are not being distributed and they do not show up in the archive.
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I have been trying with much difficulty to set up an MD simulation for a glycolipid non-covalently bound to a protein using the Amber/GLYCAM force fields. The glycolipid is digalactosyldiacylglycerol, or more specifically (2S)-3-[(6-O-a-D-galactopyranosyl-b-D-Galactopyranosyl)oxy]-2-[(3Z,6Z,9Z,12Z,15Z)-octadeca-3,6,9,12,15-pentaenoyloxy]propyl(5Z,8Z,11Z,14Z,17Z)-icosa-5,8,11,14,17-pentaenoate.
I have the 3D structure of the glycolipid from the crystallographic data for the protein complex. If I load the pdb of the glycolipid into leap, after sourcing the leaprc file for the GLYCAM force field, none of the atoms in the glycolipid are recognized. I am willing to change the atom names by hand if needed, if only I understand how to
Please post the tleap input file and the spew from tleap where it says which atoms are not recognized. Yes you'll need to change atom/residue names to match what the forcefield uses and/or load the relevant files. You may need to create your own parameters or use generic ones like GAFF (choice depends on how much accuracy you need) for the bits of the molecule that aren't currently covered. Charmm-gui has a glycolipid builder so if your glycolipid is one of the options you could build the glycolipid from scratch there and I believe they provide output in
You need to setup the lipid as per: http://ambermd.org/tutorials/advanced/tutorial16/#Lipid14_PDB_Format Lipids are not my thing, but it looks like you have named the whole molecule as one residue named JSZ. You need to break the lipid into the head and tail domains as described, then figure out which head you have and the corresponding residue in lipid14 or lipid17. tleap reads the residue name and matches up with what's in (e.g) the prep file. In this part: http://ambermd.org/tutorials/advanced/tutorial16/#Lipid14 it tells you the residue names to use and what residues it supports. Your atom names will have to match what
Thanks, Oliver! I’m very excited by your reply, and will let you know how I fair with the leads you offered.
Best, Matthew
> On Feb 18, 2021, at 11:07 AM, Oliver Grant <[log in to unmask]> wrote: > > > *Message sent from a system outside of UConn.* > > > Hi Mathew, > > You need to setup the lipid as per: http://ambermd.org/tutorials/advanced/tutorial16/#Lipid14_PDB_Format <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial16%2F%23Lipid14_PDB_Format&data=04%7C01%7CMatthew.guberman-pfeffer%40UCONN.EDU%7Ccee550450f8e4846e89a08d8d4275cc4%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637492612810785075%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=WxA3ptgeDiN2yF8TWUgSk2LOMRdA55xG4jVZ3OSNQDc%3D&reserved=0> > Lipids are not my thing, but it looks like you have named the whole molecule as one residue named JSZ. You need to break the lipid into the head and tail domains as described, then figure
I am attempting to use the Glycam Glycoprotein Builder in order to add N2M5 N-glycans to 5 sites on a specific pdb file (2B5E) for use in Amber. Everything goes well and the builder is able to identify all 5 sites I want to add glycans to. However, when I click "Download current structure" or "Download current structure without minimization", I am returned the error below. Could there be something wrong with the pdb file I am trying to use?
I can reproduce the error. We'll look into it and get back to you. I've run simulations of this system before, so you could reuse the inputs or I can send you the trajectories if you like. You'd only need to cite the paper as it's published data. Not sure what glycans I used exactly, but at least one of them is M9GN2 at each site.
On Sun, Jan 10, 2021 at 11:54 PM Trevor Matthew Adams <[log in to unmask]> wrote:
> Hi Oliver, > > I appreciate it! The trajectories of the system with N2M9 glycans would be > very useful, could you send me the trajectories? > > Thanks, > Trevor > > ------------------------------ > *From:* Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on > behalf of Oliver Grant <[log in to unmask]> > *Sent:* Friday, January 8, 2021 7:18:30 PM > *To:* [log in to unmask] <[log in to unmask]> > *Subject:* Re: Glycoprotein Builder - PDBFileNotFoundException > > [EXTERNAL SENDER - PROCEED CAUTIOUSLY] >
I am trying to use GLYCAM06_j to build carboxymethyl cellulose. However, I could not find carboxymethyl groups in GLYCAM residue list. Could anyone help me with its 3(?)-letter name?
The force field does not currently support that derivative. You will need to generate the parameters yourself.
On Mon, Nov 2, 2020 at 9:47 AM Ali Khodayari <[log in to unmask]> wrote: > > Dear GLYCAM users, > > > > I am trying to use GLYCAM06_j to build carboxymethyl cellulose. However, I could not find carboxymethyl groups in GLYCAM residue list. Could anyone help me with its 3(?)-letter name? > > > > Many thanks in advance. > > > > Kind regards, > > Ali
Can we use Glycam06 with ff14SB protein force field?
Regards, Neha
Dr. Neha S. Gandhi | Advance Queensland Senior Research Fellow School of Chemistry and Physics| Personalised Therapies (Program leader), Science and Engineering Faculty | Queensland University of Technology M-O-Block, Gardens Point Campus ph 3138 7394| email: [log in to unmask] CRICOS No 00213J
[cid:image003.jpg@01D6A78E.A513EF30] I acknowledge the Turrbal and Yugara, as the First Nations owners of the lands where QUT now stands. I pay respect to their Elders, lores, customs and creation spirits. I recognise that these lands have always been places of teaching, research and learning.
> On Oct 20, 2020, at 7:43 PM, Neha S. Gandhi <[log in to unmask]> wrote: > > [EXTERNAL SENDER - PROCEED CAUTIOUSLY] > > Dear Support, > > Can we use Glycam06 with ff14SB protein force field? > > Regards, > Neha > > Dr. Neha S. Gandhi | Advance Queensland Senior Research Fellow > School of Chemistry and Physics| Personalised Therapies (Program leader), > Science and Engineering Faculty | Queensland University of Technology > M-O-Block, Gardens Point Campus > ph 3138 7394| email: [log in to unmask] > CRICOS No 00213J > > <8492B858777E49D699E06B6015C3FA45.jpg> > I
Just make sure you use a recent version of GLYCAM06. The document at the link below explains in more detai. But, if you use the most recent version of GLYCAM06, you will be fine.
On Tue, Oct 20, 2020 at 7:52 PM Robert Woods <[log in to unmask]> wrote: > > Yes > > Excuse the brevity, sent from iPhone > > On Oct 20, 2020, at 7:43 PM, Neha S. Gandhi <[log in to unmask]> wrote: > > [EXTERNAL SENDER - PROCEED CAUTIOUSLY] > > Dear Support, > > > > Can we use Glycam06 with ff14SB protein force field? > > >
In http://glycam.org/docs/forcefield/glycam-naming-2/ Glycam Naming | Force Field<http://glycam.org/docs/forcefield/glycam-naming-2/> This page describes the three-letter code used for residue names in files relevant to the GLYCAM force fields. For information on other nomenclatures recognized by GLYCAM-Web, please click here. Current Carbohydrate Naming Convention in GLYCAM_04 and GLYCAM_06 glycam.org
the documentation states that to differentiate the conformations 1C4, 4C1 and 2SO the residue name uses a 4-letter code. You then provide the example 4uA as existing as 4uA1, 4uA2 and 4uA3 in the parameter set. However, I can't find this in the prep files included with AMBER 18 nor on the latest parameter set
The 4-letter code is not the standard prep file format for AMBER or tLEaP, so it could not be found in the AMBER18. Besides the geometry differences that are usually ignored while building models, the other differences are atomic partial charge values in those prep files.
In GLYCAM, we employ ensemble-averaged charge sets. The ensemble-averaged charge sets were derived by averaging the charge values from multiple conformation, so that the ensemble-averaged charge values could represent the averaged behavior of the sugar in solution. Therefore, we should only use one charge set for a sugar, instead of having multiple
In case there is interest I have a 10 microsecond trajectory Arixtra, which does contain an IdoA ring. Arunima and I made the trajectory. The ring conformations of IdoA did not come out in agreement with experiment. This was made 3 years ago.
Gordon Chalmers Center for Biotechnology and Interdisciplinary Studies (CBIS) Rensselaer Polytechnic Institute (RPI) Room 3235
*So how do I get the proper prep file (e.g. 4uA2) to be used, and how do I get the proper prep file at all? Do I happen across the posting from mid-2017 or am I making a big deal out of something that doesn't really matter?*
It doesn't matter if you're starting with a 3D structure (e.g from the wwPDB). The prep files allow us to generate a 3D structure in a particular ring conformation (see glycam.org/gag, and click on ring conf once you've built the sequence). However, as Xiao said, no matter what ring conf they
Hi Laura, If you want to build a GAG structure with the idoA rings in specific conformations use the GAG builder at glycam.org. You can then restrain them in those shapes during the MD if you choose.
Cheers, Rob
Excuse the brevity, sent from iPhone
> On Oct 6, 2020, at 4:15 AM, Oliver Grant <[log in to unmask]> wrote: > > [EXTERNAL SENDER - PROCEED CAUTIOUSLY] > > Hi Laura, > > So how do I get the proper prep file (e.g. 4uA2) to be used, and how do I get the proper prep file at all? Do I happen across
If this was said already, sorry for the noise: If needed, you can put the four-letter code in a PDB file and tleap will read it. The last letter goes in the space after the four-letter code. That space is not assigned in the official PDB specs. But, AMBER allows 4-character residue codes.
We are looking to find glycam parameters for an individual molecule of scyllo inositol and other stereoisomers. The glycam web interface gives blank structure (.pdb) and topology (.prmtop) files. We are unfamiliar with amber program and would like help in how to obtain these parameters.
Hi Sandra, Because inositol is not a sugar, there are no structure files for it in GLYCAM. To simulate it in AMBER, you can use GAFF and Antechamber to generate the files you need. Good luck!
Excuse the brevity, sent from iPhone
> On Sep 8, 2020, at 8:51 PM, Sandra Moore <[log in to unmask]> wrote: > > [EXTERNAL SENDER - PROCEED CAUTIOUSLY] > > > Hello Glycam users, > > We are looking to find glycam parameters for an individual molecule of scyllo inositol and other stereoisomers. The glycam web interface gives blank structure (.pdb) and topology (.prmtop) files. >
GLYCAM-Web and the Woods Group need a syadmin. This is not a scientific job, but it is science-adjacent. :-)
https://www.ugajobsearch.com/postings/160381
Excerpt:
Computer Science or a related field is preferred; a relevant scientific discipline is acceptable if the individual has sufficient experience and/or training in relevant computing systems management and design.
The preferred candidate will have experience with as many of the following general and specific infrastructure components as possible, and in time will need to have acquired at least general knowledge of them all.
I am using GLYCAM_06j-1 to build up a hemicellulose model with a backbone of xylopyranose and glucopyranosyl acid groups substituted on the backbone. The glucopyranosyl group is also methylated on the O4 atom. Hence, I am using a sequence of ROH-4XB-YXB-4ZA-MEX (bold characters are the backbone) and then the backbone ends with 4XB-0XB.
However, when I look at the glucuronic acid group, I see that on the C6 atom, there are only two O6A and O6B. I expected that one of these two oxygen must be double bonded to C6 and the other one must include a hydrogen. This
Hi, The default ionization state is the carboxylate. Good luck, Rob Woods
Excuse the brevity, sent from iPhone
> On Jun 26, 2020, at 4:15 PM, Ali Khodayari <[log in to unmask]> wrote: > > [EXTERNAL SENDER - PROCEED CAUTIOUSLY] > > Dears, > > I am using GLYCAM_06j-1 to build up a hemicellulose model with a backbone of xylopyranose and glucopyranosyl acid groups substituted on the backbone. The glucopyranosyl group is also methylated on the O4 atom. Hence, I am using a sequence of ROH-4XB-YXB-4ZA-MEX (bold characters are the backbone) and then the backbone ends with 4XB-0XB. > > However, when
Hi Ali, You can add it in tleap, but I would check the experimental pH. If it’s above about 5, then use carboxylate and add a sodium ion rather than a covalent hydrogen atom. Rob
Excuse the brevity, sent from iPhone
> On Jun 26, 2020, at 5:55 PM, Ali Khodayari <[log in to unmask]> wrote: > > [EXTERNAL SENDER - PROCEED CAUTIOUSLY] > > Dear Rob, > > Thank you for your response. > Is there any glucopyranosyl with the carboxylic acid instead of the carboxylate? > Or shall I add the hydrogen myself in leap? There is no linkage position
It’s commonly drawn with the hydrogen, but make sure the conditions are correct. In water at ph7 it will predominantly be COO-.
Best,
On Fri, 26 Jun 2020 at 23:55, Ali Khodayari < [log in to unmask]> wrote:
> Dear Rob, > > > > Thank you for your response. > > Is there any glucopyranosyl with the carboxylic acid instead of the > carboxylate? > > Or shall I add the hydrogen myself in leap? There is no linkage position > possibility on neither O6A or O6B though. > > I am trying to avoid charges to be consistent with
Thank you for your response. I’ll do the same then.
Kind regards,
Ali
From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> On Behalf Of Rob Woods Sent: Saturday, 27 June 2020 00:12 To: [log in to unmask] Subject: Re: Glucuronic acid in GLYCAM06
Hi Ali,
You can add it in tleap, but I would check the experimental pH. If it’s above about 5, then use carboxylate and add a sodium ion rather than a covalent hydrogen atom.
I think I now understand the reasoning. As GLYCAM is not a reactive force field, including the hydrogen makes it non-realistic in aquatic solutions, as it must be released eventually.
Thank you for your response.
Kind regards,
Ali
From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> On Behalf Of Oliver Grant Sent: Saturday, 27 June 2020 11:24 To: [log in to unmask] Subject: Re: Glucuronic acid in GLYCAM06
All Woods-group online resources will be unavailable for a few hours tomorrow night (Saturday, May 16, 2020, eastern time). We'll be upgrading some of the networking infrastructure.
This applies to glycam.org and to dev.glycam.org
I don't know the exact timing of the outage. All should be complete by Sunday morning, eastern time.
Sorry for any inconvenience, and ask if you have any questions.
The maintenance was completed, and I finished some details last night.
Please let us know if anything new and unexpected happens.
On Fri, May 15, 2020 at 10:30 PM Lachele Foley <[log in to unmask]> wrote: > > Hi Everyone! > > All Woods-group online resources will be unavailable for a few hours > tomorrow night (Saturday, May 16, 2020, eastern time). We'll be > upgrading some of the networking infrastructure. > > This applies to glycam.org and to dev.glycam.org > > I don't know the exact timing of the outage. All should be complete > by Sunday morning, eastern time. > >
Dear Glycam, I am interested in looking into Glucosamine parameter for NH2 and protonated residues. I have downloaded the prep files from GLYCAM. Thanks for the wonderful work. When I loaded them in the Xleap I saw that the O4 is with H(H4O) hydrogen and has a charge 0.4450. I am not aware how to link this to another acid residue. since the issue of the charge is not making integer charge.
Sorry no one has responded yet. We're all really preoccupied right now. I'll try to get to this on the weekend if someone else doesn't before.
On Tue, Mar 24, 2020 at 10:46 AM Lara rajam <[log in to unmask]> wrote: > > Dear Glycam, > I am interested in looking into Glucosamine parameter for NH2 and protonated residues. > I have downloaded the prep files from GLYCAM. Thanks for the wonderful work. > When I loaded them in the Xleap I saw that the O4 is with H(H4O) hydrogen and has a charge 0.4450. I am not aware how to link this
Do you want to use the unsaturated glucosamine residue that has a double bond between C4 and C5? If yes, then this is residue can only be the placed on the terminus (non-reducing end) of the glycan chain - this is why we do not have a version where O4- is available for connecting to the next residue. If you want the regular glucosamine residue then please use the one from the main glycam_06j-1 release available here: http://glycam.org/docs/forcefield/all-parameters/
Dear Glycam, Thanks for your reply. I want to use these protonated residues inside the sequence ( like IdoA-GlcNS6S-IdoA2S-(GlcNH3+)-IdoA2S), If so how to balance the charge and how to make glycosidic linkage, If I use the regular glucosamine. If I have understood correctly the charge on the Nitrogen need to be balanced if I am interested so? or the parameter for the specific residue available? Is it possible to give more explnation. Thanking you.
Dear Glycam I am able to understand that you guys are doing amazing work and busy at this time. I just explained my doubts in earlier emails. I am pretty sure I am able to understand the residue labeling and the parameters. I am more thinking in using Nh2 and NH3+ amines in middle of a sequence any insight will be helpful. - Thanking you in advance
Apologies for the delay. Please find the prep file for protonated glucosamine that can be used in the middle of the sequence attached. Also use this frcmod file for the parameters: http://glycam.org/docs/forcefield/wp-content/uploads/sites/6/2016/03/frcmod.glycam06_intraring_doublebond_protonatedacids
Please let me know if you have any trouble using this.
Thanks, Arunima
On Mon, Mar 30, 2020 at 5:39 PM Lara rajam <[log in to unmask]> wrote:
Dear Glycam, Thanks for the email on your busy schedule. Much appreciated. I looked into the prep file. I have a questions. when I built the heparin/heparansulfate using glycam web the residue label for N-Acetylglucosamine is 4YA. The prep file says b-D-GlcNH3p_4YP.prep. On looking the Glycam naming force field Table 4 it says alpha-D- N-Acetylglucosamine. Is the form of the sugar correct? or am I understood wrong? Also to add on is there a parameter file for NH2 form of glucosamine. - Thanking you in advance.
This parameter file should have all the necessary parameters: http://glycam.org/docs/forcefield/wp-content/uploads/sites/6/2016/03/frcmod.glycam06_intraring_doublebond_protonatedacids
And the residue is correct. Please visually also inspect it once you the the files.
Thanks, Arunima
On Tue, Mar 31, 2020 at 6:54 AM Lara rajam <[log in to unmask]> wrote:
> Dear Glycam, > Thanks for the email on your busy schedule. Much appreciated. > I looked into the prep file. I have a questions. > when I built the heparin/heparansulfate using glycam web the residue label > for N-Acetylglucosamine is 4YA. > The prep file says b-D-GlcNH3p_4YP.prep. > On looking the Glycam naming force field Table 4 it
My sincere thanks for your reply I Will definitely check and let you know. Thanks again
On Wed, Apr 1, 2020 at 10:50 AM Arunima Singh <[log in to unmask]> wrote:
> Hi Lara, > > This parameter file should have all the necessary parameters: > http://glycam.org/docs/forcefield/wp-content/uploads/sites/6/2016/03/frcmod.glycam06_intraring_doublebond_protonatedacids > > And the residue is correct. Please visually also inspect it once you the > the files. > > Thanks, > Arunima > > On Tue, Mar 31, 2020 at 6:54 AM Lara rajam <[log in to unmask]> wrote: > >> Dear Glycam, >> Thanks for the email on your busy schedule. Much appreciated. >> I looked into
Has anyone run into the following problem: I constructed alpha-methyl-D-mannopyranose with the standard GLYCAM carbohydrate builder (http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=1). I hydrated the structure in TIP3P water box (10 Angstroms x,y,z) I minimized the sugar I minimized the sugar + water box I heat the sugar to 300 K I heat the sugar + water box to 300 K I use the "...rst" file for the beginning of a 500 ns MD production run in GLYCAM06 force field.
Hi Andy, It may worth looking the script you used to exclude water molecules. In GLYCAM, OMe and sugar molecules are treated as two different residues. So, when excluding water molecules, make sure OMe (residue name OME) is included. If this is not the issue, please send me a picture or other information, so I can be more helpful. Thank you Xiao
From: Xiaocong Wang <[log in to unmask]> Sent: Monday, March 2, 2020 6:39 PM To: Users of GLYCAM & GLYCAM-Web <[log in to unmask]>; Andy Franz <[log in to unmask]> Subject: Re: MeDMan MD-simulation - help request
Hi Andy, It may worth looking the script you used to exclude water molecules. In GLYCAM, OMe and sugar molecules are treated as two different residues. So, when excluding water molecules, make sure OMe (residue name OME) is included. If this is not the issue, please send me a picture or other information, so I can be more helpful. Thank you Xiao
I am using Amber16 package and glycam force filed for MD simulation. My ligand file containing sialic acid and I substitute fluorine atom into O4 position of sialic acid. During the preparation of topology and parameter files via tleap module of Amber, I have the Fatal error as *"Atom does not have file type"* for fluorine atom. How can I parameterize fluorine atom. Thanks in Advance with regards R. A. Jeyaram Research Scholar School of Advanced Sciences Vellore Institute of Technology Tamil Nadu, India.
I haven't built force field params in a while, so others might have better (more recent) information than what I'm about to say. You will need to use GAFF for the parameters except for the partial charges. You will need to translate the parameters for the atom types in the rest of the monosaccharide. It will probably be best to generate a frcmod file containing the gaff params you need that bridge the type naming systems. After that, you will need to make a best-guess initial charge set and, based on that, compute a better, ensemble-averaged set of partial charges
Thank you very much for your valuable suggestions mam.
On Fri 23 Aug, 2019, 9:19 PM Lachele Foley, <[log in to unmask]> wrote:
> I haven't built force field params in a while, so others might have > better (more recent) information than what I'm about to say. You will > need to use GAFF for the parameters except for the partial charges. > You will need to translate the parameters for the atom types in the > rest of the monosaccharide. It will probably be best to generate a > frcmod file containing the gaff params you need that bridge the type
How are you? I'd like to ask you for some help with an antechamber issue.
I am trying to parametrize a structure but I'm having some trouble. I attach here the script. There seems to be some problem with the output file format.
On Mon, Feb 10, 2020 at 2:46 PM Alejandro Cagnoni <[log in to unmask]> wrote: > > Hi > > How are you? I'd like to ask you for some help with an antechamber issue. > > I am trying to parametrize a structure but I'm having some trouble. I attach here the script. There seems to be some problem with the output file format. > > alejandrocagnoni@julia:~/Dropbox/IBYME/colaboraciones/Lisandro Otero/paper 2019/MD$ antechamber -fi ac -i STG.ac
How are you? I'm following a thread from a couple of years ago. I've been having problems with branched oligosaccharide structures (generated from glycam web) and tleap (Amber). There is a problem with the conncetions of the atoms.
I've seen that Lachele Foley recommended to add "TER" cards on the pdb file. However, by doing so, even if I've solved the tleap problem, I have problems when minimizing the structure with sander (Amber). The monosaccharides don't remain bound to each other. Could you please help me solve this issue?
You have to issue explicit BOND commands in tleap to connect the residues back together after adding the TER cards. If you need help doing that, just say, but it's pretty easy, and there are good examples in the tleap docs.
On Mon, May 13, 2019 at 12:30 PM Alejandro Cagnoni <[log in to unmask]> wrote: > > Hi. > > How are you? I'm following a thread from a couple of years ago. I've been having problems with branched oligosaccharide structures (generated from glycam web) and tleap (Amber). There is a problem with the conncetions of the atoms. > > I've
Thank you very much. If you could please help me with the BOND command, I'd really appreciate it. If not, where can I find the tleap docs?
Thanks again
Alejandro
On Tue, May 14, 2019 at 1:30 AM Lachele Foley <[log in to unmask]> wrote:
> Hi! > > You have to issue explicit BOND commands in tleap to connect the > residues back together after adding the TER cards. If you need help > doing that, just say, but it's pretty easy, and there are good > examples in the tleap docs. > > On Mon, May 13, 2019 at
bond glyprot.125.O4 glyprot.126.C1 # make inter glycan bonds w/ source and target. bond glyprot.126.O4 glyprot.127.C1 bond glyprot.127.O6 glyprot.128.C1 bond glyprot.127.O3 glyprot.129.C1
Aarya's example is great. Off-topic, but I'd add that you can do this in every tleap input file:
addIons mol Na+ 0 addIons mol Cl- 0
Which means you don't have to think about whether your system is net positive or negative. Including both commands will bring it to neutral either way.
Also, if you change the extension names when writing out topology and restart files to this:
I'm trying to build a model for a Chitosan dimer using all the possibilities ( Deacetylated and acetylated units) as well as protonated NH3+ and deprotonated NH2 units, I've managed to build the ones where the β-D-Glucosamine and the protonated β-D-Glucosamine are terminals, and I have also found in this mailing list a prep file provided by Arunima for the non-terminal protonated version, whereas I also need a non-terminal β-D-Glucosamine connected by means of β 1 -> 4 linkages.
So i'm building a protonated version of Hyaluronic Acid, i succeeded in building one unit where there is the terminal protonated version of the β-D-glucuronic acid (0ZBP) , now i want to build a dimer of hyaluronic acid so i want the protonated version of a non-terminal β-D-glucuronic acid (4ZBP) connected by means of β 1 -> 4 linkages. I wanted to know if it's possible to build it by my self using with the files available in the website. Thank you
Please find the prep file attached. Let me know if you have any problem using it.
Best, Arunima
On Tue, Mar 26, 2019 at 7:24 AM Monia Kam <[log in to unmask]> wrote:
> Hello Glycam users and developpers, > > So i'm building a protonated version of Hyaluronic Acid, i succeeded in > building one unit where there is the terminal protonated version of the > β-D-glucuronic acid (0ZBP) , now i want to build a dimer of hyaluronic acid > so i want the protonated version of a non-terminal β-D-glucuronic acid > (4ZBP) connected by means of β 1
Le mardi 26 mars 2019, Arunima Singh <[log in to unmask]> a écrit :
> Hi Monia, > > Please find the prep file attached. Let me know if you have any problem > using it. > > Best, > Arunima > > > On Tue, Mar 26, 2019 at 7:24 AM Monia Kam <[log in to unmask]> wrote: > >> Hello Glycam users and developpers, >> >> So i'm building a protonated version of Hyaluronic Acid, i succeeded in >> building one unit where there is the terminal protonated version of the
Placement of the O3 is incorrect. Minimization might fix what you've got, but looks like a problem with the prep file. Oliver
On Tue, Apr 2, 2019 at 2:00 PM monia kam <[log in to unmask]> wrote:
> Hello Arunima, > > So i tried to use your prep file to generate a protonated Hyaluronic acid > using linkage 1,4 but i think there is something wrong with the structure > when viewing it using VMD. > Here is my pdb file, i tried to fix it but i couldn't, hope you can help > me. > > Le mar. 26 mars 2019
So i tried to use your prep file to generate a protonated Hyaluronic acid using linkage 1,4 but i think there is something wrong with the structure when viewing it using VMD. Here is my pdb file, i tried to fix it but i couldn't, hope you can help me.
Le mar. 26 mars 2019 à 20:19, monia kam <[log in to unmask]> a écrit :
Yeah exactly there is a problem with the prep file and i coudn't fix it, when i tried minimization to fix what i've got i got the errors No default Bond, Angle and Improper Dih. types
Le mar. 2 avr. 2019 à 14:07, Oliver Grant <[log in to unmask]> a écrit :
> Placement of the O3 is incorrect. Minimization might fix what you've got, > but looks like a problem with the prep file. > Oliver > > > On Tue, Apr 2, 2019 at 2:00 PM monia kam <[log in to unmask]> wrote: > >> Hello Arunima, >> >> So i tried
Because i'am working with Gromacs, I actually used do_glycans ( a python script) using the prep file to generate the pdb and itp files, in the Glycam website i only found the terminal protonated version of the β-D-glucuronic acid (0ZBP) while for my case i wanted the non_terminal one, so Arunima sent a prep file.
Dear Monia, how did you prepare the input? Did you also load the additional .frcmod file? I do not remember if Arunima has sent this to you, but it is available in the Glycam website. Best T
I have checked the prep file for protonated GlcA, and so has another colleague. Please see the attached pdb, prmtop and restart files. The structures we built on our end have all the right connections, and I am not able to figure out where the problem on your end originated from.
Also, see an example leap input file for your reference. You will of course need to change the paths according to your system set up. See if you can figure out what you might be doing differently in your input file.
Wow thank you very much for your help, I'll check all the files on monday and I'll let you know, thank you again
Le vendredi 12 avril 2019, Arunima Singh <[log in to unmask]> a écrit :
> Hi Monia, > > I have checked the prep file for protonated GlcA, and so has another > colleague. Please see the attached pdb, prmtop and restart files. The > structures we built on our end have all the right connections, and I am not > able to figure out where the problem on your end originated from. > > Also, see an
Hello, So i actually have an issue with the protonated version of Beta-D-Glucuronic acid for the construction of the model hyaluronic acid, so i included the version 0ZBP in the prep file GLYCAM06.prep, but then i got these following errors with grompp: ERROR 1 [file HAP.itp, line 104]: No default Bond types
ERROR 2 [file HAP.itp, line 325]: No default Angle types
Thank you .That was really helpful, i'll try to reach out for more help with the guys who made do_glycans. If it doesn't work i'll try using Amber as you recommended.
Le mer. 20 mars 2019 à 14:12, Oliver Grant <[log in to unmask]> a écrit :
> Dear Monia, > > I haven't used gromacs in years so I can't help you much, and no one else > currently the Woods group has used it that I'm aware of. I haven't heard of > do_glycans, but I looked it up. The research group ( > https://www.helsinki.fi/en/researchgroups/biophysics) that made it has
I haven't used gromacs in years so I can't help you much, and no one else currently the Woods group has used it that I'm aware of. I haven't heard of do_glycans, but I looked it up. The research group ( https://www.helsinki.fi/en/researchgroups/biophysics) that made it has published this: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005663 , where they do indeed use Glycam/Amber within gromacs. That has risks as you must convert properly, and it's easy to do it incorrectly and not notice.
You can prepare the system with the tleap module of AmberTools, where you can load the additional .prep file for protonated glucuronic acid and the additional frcmod as well. It is possible to convert the final topology and coordinate files with parmed.py (included in AmberTools, if I remember correctly) or other validated tools such as acpype.
Le mer. 20 mars 2019 à 15:36, Casalini Tommaso < [log in to unmask]> a écrit :
> Dear Monia, > let me add something. > > You can prepare the system with the tleap module of AmberTools, where you > can load the additional .prep file for protonated glucuronic acid and the > additional frcmod as well. > It is possible to convert the final topology and coordinate files with > parmed.py (included in AmberTools, if I remember correctly) or other > validated tools such as acpype. > > Anyway, you must be
Dear GLYCAM users and developers, I need to simulate a chitosan chain. I see that you have already developed and validated FF parameters and charges for protonated β-D-Glucosamine (Singh et al. paper), and .prep files are available on GLYCAM website. Assuming that I made no mistakes, only terminal residues are available, while I need also a non - terminal protonated β-D-Glucosamine connected by means of β 1 -> 4 linkages. Can I obtain such unit with the available files, or should I recompute the charges by myself? I thank you for your help and collaboration. With my best regards, Tommaso
The GAG builder (glycam.org/gag) Arunima made doesn't handle Chitosan, which would make this easy. But as you say there are parameters and prep files available. The residue you want is 0YNp, but yes it looks like this isn't available on the regular builder (glycam.org/cb) either. In that case I recommend you build something similar and edit. I.e. build: DGlcpNAcb1-4DGlcpNAcb1-OME on glycam.org/cb and download the PDB file. This will give you a reasonable geometry to work with. Delete the Ac group from whichever residues you need be protonated GlcN E.g.: remove these atoms: HETATM 25 H2N 4YB 2 5.762
We have the charges and parameters for the non - terminal protonated β-D-Glucosamine (β 1 -> 4 linkages) available. Please find the prep files and associated parameters attached.
Let me know if there's any problem using these.
Best, Arunima
On Tue, Mar 12, 2019 at 9:02 AM Oliver Grant <[log in to unmask]> wrote:
> Hi Tommaso, > > The GAG builder (glycam.org/gag) Arunima made doesn't handle Chitosan, > which would make this easy. But as you say there are parameters and prep > files available. The residue you want is 0YNp, but yes it looks like this > isn't available
Dear Arunima, thanks a lot for your mail and your parameters! Very appreciated. I have a couple of questions:
1) I checked the .prep files, and atom types seem to be AMBER ones and not GLYCAM ones (e.g., CG against Cg). Is there a reason for this? 2) The overall charge of the unit is 1.1940, I expected 1.00. In addition, if I import the file in tleap and if I type "desc" to check head and tail, I see that they are C1 and C2, respectively.Am I missing something, in order to convert this unit to the 1-4 one?
I'm sorry, there seems to be a mixup here. Let me check the files and get back to you. Oliver's suggestions still work though, and yes you would need the Glycam atom types.
On Tue, Mar 12, 2019 at 11:08 AM Casalini Tommaso < [log in to unmask]> wrote:
> Dear Arunima, > thanks a lot for your mail and your parameters! Very appreciated. > I have a couple of questions: > > 1) I checked the .prep files, and atom types seem to be AMBER ones and not > GLYCAM ones (e.g., CG against Cg). Is there a reason for this? >
Please find the correct file attached, and feel free to let me know if you face any other problems with it.
Best regards, Arunima
On Tue, Mar 12, 2019 at 11:48 AM Arunima Singh <[log in to unmask]> wrote:
> I'm sorry, there seems to be a mixup here. Let me check the files and get > back to you. Oliver's suggestions still work though, and yes you would need > the Glycam atom types. > > On Tue, Mar 12, 2019 at 11:08 AM Casalini Tommaso < > [log in to unmask]> wrote: > >> Dear Arunima, >> thanks a lot for your
Dear Arunima, thanks for the file!! I implemented also the suggestion from Oliver and everything went well.
I took the terminal unit from the .prep file available on GLYCAM website. Also in this case, if I use the command "desc", it seems that head and tail atoms are C1 and C2, respectively. I changed the name of the residue to 0YP and I manually removed the tail atom with tleap, with the command:
Hello all, I have proposed a different question earlier relating to the above subject and managed to model my non-standard sugar and run a simulation successfully. As per now, I have a doubt as to did I model properly. Because my structure is a transition state implying the properties of a non-standard sugar ie. a glucose molecule with anomeric -O connected to a cyanogenic moiety. Thus I modeled the cyanogenic portion with a separate parameter file (frcmod) and provided GLYCAM_06j-1 for the sugar portion (named and numbered correctly). Yet as per my understanding GLYCAM forcefield describes equilibrium bond and angle
Hi Senal, If you have a distorted ground-state (such as may be present in a Michaelis complex, or a TS-like mimetic) then GLYCAM may handle it fine. There are no constraints that prevent ring flexion in GLYCAM. Classical force fields in general are unable to handle the partial bonds present in a true transition state. However, when you introduce new atom types or linkages, there is always a need to carefully examine the electrostatic model and the valence parameters. Good luck, Rob
ERROR: Comparing atoms .R<0ZB 8>.A<C2 17>, .R<0ZB 8>.A<H1 2>, .R<0ZB 8>.A<O5 3>, and .R<4YS 7>.A<O4 25> to atoms .R<0ZB 8>.A<C2 17>, .R<SO3 1>.A<S1 1>, .R<0ZB 8>.A<O5 3>, and .R<4YS 7>.A<O4 25> This error may be due to faulty Connection atoms. !FATAL ERROR---------------------------------------- !FATAL: In file [chirality.c], line 142 !FATAL: Message: Atom named S1 from SO3 did not match !
tleap was designed for linear sequences of residues like in protein molecules, so it auto-bonds each residue in the sequence it encounters them when reading a PDB file. For branched molecules, you must place a TER card between the residues that should not be bonded to each other (edit the PDB file and literally create a new line with the word "TER", between the residues), and then use the "bond" command in tleap to connect the correct residues to each other. E.g:
Hello to everyone, I would like to ‘properly’ describe a trimannoside which is fluorinated at position 2 (the fluorine substitutes the OH) in each monomer. I know that the ‘easiest’ way of doing so is just by using GAFF… but in that case I would lose all the special sugar-related chemistry that is modeled in GLYCAM. For that purpose, I thought of adding a .frcmod file to use in combination with GLYCAM force field. In such .frcmod file, I would include the necessary parameters from GAFF (gaff2.dat). I would like to combine both force fields, if possible, in order to
I have only vague advice for you. I have mixed GAFF and GLYCAM using a frcmod where I picked the best parameters I could find. However the accuracy required for the application was quite low (very simplistic modeling) so I could defend what I did. You'll have to figure that out based on what you plan to use the results for. You can describe the project here if you like. To do it "properly" you must develop charges as done for GLYCAM. I see you've been recommended here from this http://archive.ambermd.org/201811/0288.html.
I am a new user to Glycam and I am trying to build glycoprotein by submitting a pentamer on Glycam server. However, Glycam only recognizes one peptide with two terminals. Is there any specification on how Glycam server recognizes monomer units?
I also need disulfide bonds built. Submitting a pentamer directly will therefore make things much more convenient.
We need some clarification. Is the pentamer you speak of a peptide made of five amino acids? If not that, then please specify.
If you want to attach a glycan to a single, zwitterionic, amino acid, GLYCAM has, available for this purpose, variants of serine and threonine (residue names ZOLS and ZOLT). If you want to model any other amino acids, or if you don't want the zwitterionic form, you will need to generate a residue with partial atomic charges.
If I interpreted correct, perhaps protomer is the word to use instead of peptide. In a PDB file sometimes each protomer of an oligomer will have MODEL and END cards between each protomer. Try removing them. You can also load the PDB file into something like USCF Chimera and rename the chains and/or renumber the residues to be contiguous.
Thanks for your reply. My "pentamer" is a heteromer which is consisted of two identical heterodimers and one monomer. They are not bonded covalently but through van der Waal's interaction. I managed to solve it by appending TER between each monomer. Now Glycam server can recognize them perfectly.
Regards, Simon Kit Sang Chu Ph.D. student Biophysics Graduate Group University of California Davis
Yes, that would make a difference. :-) Glad you got it worked out, and thank you very much for sharing your solution here!
On Mon, Nov 5, 2018 at 6:26 PM Kit Sang Chu <[log in to unmask]> wrote:
> Hi Oliver and Lachele, > > Thanks for your reply. My "pentamer" is a heteromer which is consisted of > two identical heterodimers and one monomer. They are not bonded covalently > but through van der Waal's interaction. I managed to solve it by appending > TER between each monomer. Now Glycam server can recognize them perfectly. > > Regards, > Simon Kit
I am attempting to run an MD in GROMACS on a co-crystallized Glycosyltransferase containing a carbohydrate ligand bound.
The ligand is a-L-Fucp-(1-2)-B-D-Galp.
My structure is 1LZJ is from: https://www.rcsb.org/structure/1LZJ
To parametrize this ligand, I am using a combination of tleap and either acpype or Glycam2gmx.pl to convert the amber parm/crd outputs into gromacs format, but neither are giving me working input files (fails at generating ions due to topology incompatibility/Glycam2gmx output finds no residues, where acpype does find residues).
Don't use acpype, unless they have explicitly said that they've updated it to work with GLYCAM. Some terms won't get converted.
You can build the structure on glycam.org/cb and click "download all structures". You'll get the parameter and rst files in the zip file.
The sequence command in leap is for building from prep files. You could do it that way if you want. But note it should be: { ROH 2LB 0fA }. 1fA doesn't make sense there. More detailed examples are the amber manual.
I see you have a co-complex, so building the carbohydrate on glycam.org won't help you. Nor will building from sequence. You'll need to reformat the carbohydrate in 1LZJ in GLYCAM nomenclature so that tleap can recognise it and bond it correctly. Try reorganizing the atoms so the autobonding works. Send all the output from tleap if not.
This might be the cause of the issue. I believe that rdparm has been deprecated in recent versions of AMBER.
Other than that, the following output says that your pdb file isn't formatted correctly. Specifically, the residue 2LB needs to be a different number from residue ROH. The complaints about residues 264 and 282 are also important.
We are trying to simulate polysaccharides, cellulose and hemicellulose in particular, in GROMACS. The intention is to use GLYCAM forcefield parameters as well.
My question is, is there any properly quick way to parametrize GLYCAM force field to be used in GROMACS?
Moreover, is it feasible to manually write the raw force field parameters (GLYCAM_06j.dat) in GROMACS language? Let's say, using a python script? Or it leads to any further problems?
It was possible to build an amber topology file and convert it to gromacs. Here's what I knew in 2015 (I don't use gromacs anymore). You'll need to validate your converted topology, as I've seen months of simulations wasted. For sure don't use amb2gmx.pl or ACPYPE. Marko Wehle's script (see attached) did work in 2012, but I do not recommend anyone does this. Gromacs is constantly changing and Marko's script is no longer being maintained. Further, the whole process adds an extra layer of complexity, increasing your chances of getting garbage. I'm attaching Marko's scripts here anyway, but
Dear Mr./Mrs. We are trying to build “heparin sulfate octasaccharide” using its GLYCAM website (GAG builder Heparin/Heparan sulfate) and use it with AMBER-16 and xleap; but by the moment, this is impossible. Exactly, we are using the next sequence: DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4-OH The problem is in the residue DGlcpNS[3S]a1 (named by GLYCAM builder as ‘6YS’), which is not detected in xleap and the following message appears (The GYS residue is unknown):
You need more prep files. Go to the site below and look in the "Special Releases" section. You need the GlcNS prep file. Load that in your leap session.
On Mon, Oct 22, 2018 at 4:48 AM Javier Lopez <[log in to unmask]> wrote:
> Dear Mr./Mrs. > We are trying to build “heparin sulfate octasaccharide” using its GLYCAM > website (GAG builder Heparin/Heparan sulfate) and use it with AMBER-16 and > xleap; but by the moment, this is impossible. > Exactly, we are using the next sequence: > > DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4-OH > The problem is in the residue DGlcpNS[3S]a1 (named by GLYCAM
On Thu, Oct 25, 2018 at 11:34 AM Lachele Foley <[log in to unmask]> wrote:
> Hi! > > You need more prep files. Go to the site below and look in the "Special > Releases" section. You need the GlcNS prep file. Load that in your leap > session. > > > On Mon, Oct 22, 2018 at 4:48 AM Javier Lopez <[log in to unmask]> > wrote: > >> Dear Mr./Mrs. >> We are trying to build “heparin sulfate octasaccharide” using its GLYCAM >> website (GAG builder Heparin/Heparan sulfate) and use it with AMBER-16 and >> xleap; but
Dear Mr./Mrs. We are trying to build “heparin sulfate octasaccharide” using its GLYCAM website (GAG builder Heparin/Heparan sulfate) and use it with AMBER-16 and xleap; but by the moment, this is impossible. Exactly, we are using the next sequence: DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4-OH The problem is in the residue DGlcpNS[3S]a1 (named by GLYCAM builder as ‘6YS’), which is not detected in xleap and the following message appears (The YS residue is unknown):
The latest parameters are attached. The prep file contains a 6YS.
Best, Oliver
On Mon, Oct 22, 2018 at 10:43 AM Javier Lopez <[log in to unmask]> wrote:
> Dear Mr./Mrs. > We are trying to build “heparin sulfate octasaccharide” using its GLYCAM > website (GAG builder Heparin/Heparan sulfate) and use it with AMBER-16 and > xleap; but by the moment, this is impossible. > Exactly, we are using the next sequence: > > DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4-OH > The problem is in the residue DGlcpNS[3S]a1 (named by GLYCAM builder as > ‘6YS’), which is not detected in xleap and the following message appears
On Mon, Oct 22, 2018 at 4:53 AM Oliver Grant <[log in to unmask]> wrote:
> Hi Javi, > > The latest parameters are attached. The prep file contains a 6YS. > > Best, > Oliver > > > On Mon, Oct 22, 2018 at 10:43 AM Javier Lopez <[log in to unmask]> > wrote: > >> Dear Mr./Mrs. >> We are trying to build “heparin sulfate octasaccharide” using its GLYCAM >> website (GAG builder Heparin/Heparan sulfate) and use it with AMBER-16 and >> xleap; but by the moment, this is impossible. >> Exactly, we are using the next sequence: >> >>
I have been trying to simulate a cyanogenic glucoside (linamarin) bound protein with AMBER. Since GLYCAM doesn't offer parameters for a cyanogenic moiety I renamed the sugar portion as "0GB" to comply with GLYCAM residue naming and the rest of the ligand "UNK". But so far I was unable to generate parameters for the entire system successfully. Am I following a correct approach? I appreciate any guidance on handling this matter
I don't think GLYCAM has parameters for cyano group. I suggest that you use gaff for cyanogenic moiety. You also need atomic charges for your molecules. Please check GLYCAM06 paper for procedures to derive charges for molecules in GLYCAM06.
Best regards,
Xiao
Xiaocong Wang Complex Carbohydrate Research Center The University of Georgia 315 Riverbend Road, Athens, GA, 30602 Tel: (706) 254-7958 E-mail: [log in to unmask]
I would like to simulate several galactose derivatives bound to a protein. I would like to proceed with a QM parametrization by using gaussian to optimize the geometry and calculate the ESP and then use the AMBER tools to fit resp charges and generate the parameter sets for simulating with the AMBER ff.
This question belongs a bit in both lists - AMBER and GLYCAM.
So, first the AMBER-level question: What is the amino acid to which you want to attach the galactose? What are the types of galactose derivative? It might be that the parameters you need already exist.
If you do need to develop the params, then we'll switch to the GLYCAM list where you are likely to get a more detailed response.
I was wondering if anyone had a prep file for the b1-6 linkage form of the GlcNH2 residue (i.e. 6YN)? The prep files supplied through GlycamWeb only have 0YN/n topologies.
Hi Andrew, It is very strange that we have 0YN, but not 6YN. I have put this request on the list, for our next update of GLYCAM force field. If you need to build the 1-6 linkage GlcNH2 now, you can modify the 0YN through tLEaP. Several steps to do that through tLEaP:
I was wondering if a stand alone version of the carbohydrate and glycoprotein builders exist ? We are involved in glycobiology and molecular modeling and we would be interested in installing these programs on our cluster.
They will exist shortly. Preliminary versions exist, but they still need tweaking and testing.
These versions will be command-line utilities, not graphical interfaces.
On Fri, Sep 14, 2018 at 12:26 PM Jerome de Ruyck < [log in to unmask]> wrote:
> Dear, > > I was wondering if a stand alone version of the carbohydrate and > glycoprotein builders exist ? We are involved in glycobiology and molecular > modeling and we would be interested in installing these programs on our > cluster. > > Thanks for your answer ! > > Sincerely, > > de Ruyck Jerome
We’re carrying out some studies on chemically modified sialic acids - specifically N-acetylation at the C4, C7, C8, or C9 positions. Because there are many potential acetylation sites, we became interested in questions such as: (1) how much do the charges depend on the N-acetylation site, and (2) how much does the N-acetylation affect the charges on the sialic acid itself.
Your procedure is the same as what we did for deriving ensemble-averaged partial atomic charge sets for carbohydrate molecules. It is a very thorough work for reproducing charge sets for 0SA. I have two questions about calculation detail: 1. What level of theories did you use for geometry optimization and ESP calculation? 2. In step 6, by "aliphatic hydrogens", you mean all aliphatic hydrogen atoms in 0SA+OME, not just those in OME?
1) We used HF/6-31G* for constrained energy minimization and also for the ESP calculations.
2) We set the charges on certain hydrogens in 0SA to zero, based on whether they were bonded to carbon. The atom names are: H3E, H3A, H4, H5, H6, H7, H8, H9S, H9R, H3M, H2M, H1M. I think these are the same hydrogens that got zero charges in GLYCAM. For OME we froze all of the charges and did not optimize them at all, which meant hydrogens H1, H2, H3 had charges of zero in the calculation.
Hi Dr. Wang, We usually have HF/6-311+G** for sugars with charges (both geometry optimization and ESP calculations). I am not sure if this would be the problem. I have the same thoughts for where the problems might also be. I usually don’t see ring distortion like that. But, I did not derive charges for sialic acid. I will ask around for people in our lab who have worked on this sugar to see if the ring distortion in it is common. Thank you! Best regards, Xiao
The use of different basis sets is one possible source of the difference. I based the choice of using 6-31G* on the following:
From the 2007 GLYCAM paper, there is the quote “For each of these snapshots partial charges were calculated by fitting to the HF/6-31G* MEP. Prior to the charge calculations, each structure was optimized at the HF/6-31G* level, with the rotatable exocyclic bonds constrained to their MD conformations.” In addition, the RED server also uses this basis set to derive GLYCAM charges:
In the course of an MD simulation, it is common to encounter structures that are not at a local minimum. If a structure is flexible - that is, if its energy landscape is 'flatter' - then it might stray quite far from local minima. I am not familiar with the finer details of sialylate's ring-puckering prefeences, but its electronic structure causes it to have other interesting conformational proclivities, notably increased flexibility in the psi dihedral (the exo-anomeric effect).
Thank you very much for your feedback. I was traveling for a few days, sorry for the slow response. The large distortions in the ring (after constrained energy minimization at HF/6-31G*) are quite common for this system. I expect they may become even more common if we add more chemical substitutions.
I will try two approaches and get back to you with results: (1) Constraining the ring dihedral angles in addition to the exocyclic ones when doing energy minimization; and (2) including diffuse functions in the basis set when minimizing and computing the ESP.
I’m writing back with an update - we tried a few modifications to the procedure I described to derive the sialic acid charges. The “original” procedure is described earlier in the thread, and each test involves changing only one thing in the whole procedure. Here are some RMS errors, comparing the charges we derived vs. the charges in GLYCAM.
Having spoken with a group member who derives charges a lot, that is probably a reasonable deviation. I'll try to find the data for the charge derivation that was done here. If I can find it, I can get you a more solid statistics-based answer.
On Wed, Aug 8, 2018 at 11:42 PM Lee-Ping Wang <[log in to unmask]> wrote:
I am trying to simulate below mentioned ligand (linamarin) docked to b-Glucoside enzyme. It is made up of a glucose moiety in which anomeric O-H is substituted by a cyanogenic moitey. I would like to know if one would necessarily require the use GLYCAM force-field to model such system. If so how to prepare the PDB/mol2 file to comply with GLYCAM naming conventions.
GLYCAM is a general biomolecular force field, but designed and developed based on carbohydrate molecules. It has been tested by the research community for its accuracy on representing the properties of carbohydrate molecules. There are also many other force fields that can model carbohydrates and other biomolecules (DOI: 10.1002/wcms.89<http://sci-hub.tw/10.1002/wcms.89>).
I have a 5-sugar units chain in my molecule and I want to substitute sulfate at all the positions but when I try to add sulfate as a derivative on the end terminal sugar, it always gives free OH at position 1 of sugar using "carbohydrate builder” option. If I download that file and add sulfate by replacing OH, the charge of sulfate will still be +0.194 as it was of OH but the charge of sulfate should be same as of other sulfates. If there is any possible way to design a fully sulfated carbohydrate, please suggest.
Just to be sure I understand: You want to sulfate the monosaccharide at all positions including the anomeric position? You can't do that with the builder, but it can be done using tleap. Are you familiar with tleap?
I don't recall the status of the phosphate derivative development, but it isn't ready. Anyone know the status?
Mohit works with me, and he is acquainted using tleap in AMBER.
If I remember the charge correctly on anomeric position (OH) is -0.194. If we add sulphate at this position, how are the charges taken into account at the anomeric position?
GLYCAM has parameters for phosphate but not the charges.
We haven't tested phosphate charges explicitly, that's why we haven't released charges for phosphate on our webtool.
Best,
Xiao
Xiaocong Wang Complex Carbohydrate Research Center The University of Georgia 315 Riverbend Road, Athens, GA, 30602 Tel: (706) 254-7958 E-mail: [log in to unmask]
On Tue, Jun 12, 2018 at 9:48 PM, Xiaocong Wang <[log in to unmask]> wrote:
> Hi Neha, > > We haven't tested phosphate charges explicitly, that's why we haven't > released charges for phosphate on our webtool. > > Best, > > Xiao > > > Xiaocong Wang > Complex Carbohydrate Research Center > The University of Georgia > <https://maps.google.com/?q=Georgia+%0D%0A+315+Riverbend+Road,+%0D%0A+Athens,+GA,+30602&entry=gmail&source=g> > 315 Riverbend Road, > <https://maps.google.com/?q=Georgia+%0D%0A+315+Riverbend+Road,+%0D%0A+Athens,+GA,+30602&entry=gmail&source=g> > Athens, GA, 30602 > <https://maps.google.com/?q=Georgia+%0D%0A+315+Riverbend+Road,+%0D%0A+Athens,+GA,+30602&entry=gmail&source=g> > Tel: (706) 254-7958 > E-mail: [log in to unmask] > ------------------------------ > *From:* Users of GLYCAM
I have replaced hydroxy at the anomeric position to Sulfate and able to adjust the charges. I have difficulty with the residue name. My first sugar is PGB (PDB file is attached for your perusal). Glycam06j_1 doesn't include O1 in the PGB residue. How should I name the residue consisting of oxygen "O1" that is linked to PGB?
Off the top of my head, you have three options. I'll let you decide which is less painful.
1. Make yourself a new PGA-like residue, call it whatever you like (999, XYZ, etc.). It's just like PGA, but it includes O1. To simplify construction of this residue, try starting with the 1GA residue - to get the internal coordinates right - then remove hydrogens as needed and adjust oxygen charges to match those in PGA.
I downloaded and unzipped vina-carb but I get an error when I try to run it. There's no readme (excluding the license file) so I'm not sure how I would compile it if that's what I need to do. The output is:
The instructions for compilation/installation are here: http://glycam.org/docs/othertoolsservice/download-docs/publication-materials/vina-carb/ It looks like you missed at least this step:
- - The environment variable VINA_CARB should be set to point to the location of parent directory VC_1_0. Please provide the full path.
In bash you'd do that by: export VINA_CARB=your/path/here/VC_1_0 for example on my machine: export VINA_CARB=/home/oliver/Programs/VC_1_0
To make that a permanent variable, you can add the export line to your .bashrc file (or equivalent).
I couldn't find the page you referenced (on my own). When I went to the publication materials I didn't see it nor did I see any reference to it anywhere else.
Do you think someone could put a link in the block that has the link (etc.) for the program? I've seen it in other blocks, most notably BFMP.
We are required to substitute sulphate with phosphate. There are parameters (atom type, bond length, angles and torsions) for phosphate but not the charge. I was wondering if we can add phosphate as a derivative at position 6 to the a-Mannose and simulate this using GLYCAM.
There is a discussion of this on the AMBER reflector from 2014. The title of the thread is "Glycophosphate parametrization using GLYCAM". In summary:
*Lachele: "There are parameters except for the charges. You would need to generate ensemble-averaged charges for the phosphated residues you plan to simulate."*
I don't think we've developed anything for phosphates in the meantime.
On Tue, May 22, 2018 at 3:57 AM, Oliver Grant <[log in to unmask]> wrote:
> Hi Neha, > > There is a discussion of this on the AMBER reflector from 2014. The title > of the thread is "Glycophosphate parametrization using GLYCAM". > In summary: > > *Lachele: "There are parameters except for the charges. You would need to > generate ensemble-averaged charges for the phosphated residues you plan to > simulate."* > > I don't think we've developed anything for phosphates in the meantime. > > Oliver > > On Tue, May 22, 2018 at 3:01 AM,
I tried to generate the parameters for Fondaparinux (Arixtra), in which the sequence is D-GlcNS6S-α-(1,4)-D-GlcA-β-(1,4)-D-GlcNS3,6S-α-(1,4)-L-IdoA2S-α-(1,4)-D-GlcNS6S-OMe, by using GLYCAM web server. First, I had the problems that residue UYS, QYS, and 6YS don't have parameters in the GLYCAM_06j-1.prep file. However, I found updated parameters for GLYCAM (GLYCAM_06k.prep) and all parameters for these residues can be found in leaprc.GLYCAM_06k. But then I have another problems during tleap (in AMBER), I got this warning about charges
Hi Kanin, Try using the gag builder tool: http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=8
Best wishes, Rob
Excuse the brevity, sent from iPhone
> On Apr 24, 2018, at 1:17 PM, Kanin Wichapong <[log in to unmask]> wrote: > > Dear Sir, > > I tried to generate the parameters for Fondaparinux (Arixtra), in which the sequence is D-GlcNS6S-α-(1,4)-D-GlcA-β-(1,4)-D-GlcNS3,6S-α-(1,4)-L-IdoA2S-α-(1,4)-D-GlcNS6S-OMe, by using GLYCAM web server. First, I had the problems that residue UYS, QYS, and 6YS don't have parameters in the GLYCAM_06j-1.prep file. However, I found updated parameters for GLYCAM (GLYCAM_06k.prep) and all parameters for these residues can be found in leaprc.GLYCAM_06k. But then I have another problems during
Old, but maybe useful: http://glycam.org/old/pages/sulfation.html
Oliver
On Tue, Apr 24, 2018 at 7:58 PM, Rob Woods <[log in to unmask]> wrote:
> Hi Kanin, > Try using the gag builder tool: http://glycam.org/tools/ > molecular-dynamics/oligosaccharide-builder/build-glycan?id=8 > > Best wishes, > Rob > > Excuse the brevity, sent from iPhone > > On Apr 24, 2018, at 1:17 PM, Kanin Wichapong <[log in to unmask]> > wrote: > > Dear Sir, > > I tried to generate the parameters for Fondaparinux
Yes, I use the gag builder tool to build the heparin but first I have the problems about the naming and parameters of some residues (e.g. (UYS, QYS, and 6YS) that parameter of these residues cannot be found in GLYCAM_06j-1.prep and leaprc.GLYCAM_06j-1. Then, I use the updated glycam parameters (leaprc.GLYCAM_06k and GLYCAM_06k.prep) and parameters of these residues can be found in these new parameter files (leaprc.GLYCAM_06k and GLYCAM_06k.prep). However, I got another problems that the total charge is not 0. But I can solve the problems now.
Yes. You can also find out what the charge is by running tleap once and using the charge command, eg: charge mol.4.O6 But checking the prep is fine too.
Oliver
On Wed, Apr 25, 2018 at 1:23 PM, Kanin Wichapong <[log in to unmask]> wrote:
> Dear Rob and Oliver, > > Thank you so much for your helps and suggestions. > > Yes, I use the gag builder tool to build the heparin but first I have the > problems about the naming and parameters of some residues (e.g. (UYS, QYS, > and 6YS) that parameter of these residues cannot
I have modelled sulphated heparin tetrasaccharide using GLYCAM server. I want to attach lipophilic groups at one of the ends of the tetrasaccharide. Can I use GAFF force-field with AM1/PM3 charges for the lipophilic groups or chain-like (CH2)n? Or am I required to derive RESP charges for the fragment?
It depends on the application. I've used mixed GAFF and GLYCAM before whenever I wanted to generate some *possible *shapes of an aglycone, and I didn't care about accurately computing the populations of those shapes. The application was quite low accuracy, so I was comfortable using GAFF.
Best,
Oliver
On Fri, Apr 6, 2018 at 2:22 AM, Neha S. Gandhi <[log in to unmask]> wrote:
tleap doesn't automatically handle branching, and will bond each residue to each following residue as it reads it from the pdb file. So you can put a line that says TER in the pdb file in between the parts of your structure that is branched and then use tleap bond commands to bond the parts you want bonded.
On Sun, Apr 1, 2018 at 3:22 AM, Oliver Grant <[log in to unmask]> wrote:
> Hi Tarsis, > > tleap doesn't automatically handle branching, and will bond each residue > to each following residue as it reads it from the pdb file. So you can put > a line that says TER in the pdb file in between the parts of your structure > that is branched and then use tleap bond commands to bond the parts you > want bonded. > > The way I do it is to put
Hi, I would like to ask if anyone know why I am not getting the complete structure (pdb format after minimization) of my glycan. This is my condensed structure notation ...
Ph.D. (Computational Biophysics) Research Scholar BioSciences and Biomedical Engineering (BSBE) Indian Institute of Technology, Indore India Mob: +919732000302/+917417640425
The difference is the Neu5Ac2, you had a 1, which is incorrect, and a p, which is correct but the builder didn't like it. That's a problem on our side. The point and click interface would not have created this structure, and when you manually enter structures I guess there isn't a check for this problem. I'd suggest looking in the oligosaccharide libraries we have on the site and editing those to what you need. Less chance of a problem.
I would like to ask if anyone knows or have cpptraj or ptraj scripts that would facilitate high-throughput analysis of oligosaccharides trajectories as the ones found at CAT (torsion angles, conformational maps, rotation profiles, etc).
cpptraj would be able to calculate bond length, angle, and torsion angles easily.
The key words are following:
bond length -- "distance"
bond angle -- "angle"
torsion angle -- "dihedral"
Sincerely,
Xiao
Xiaocong Wang Complex Carbohydrate Research Center The University of Georgia 315 Riverbend Road, Athens, GA, 30602 Tel: (706) 254-7958 E-mail: [log in to unmask]
CAT was created as these types of analysis aren't straight forward to do. It has very nice features, but a learning curve. The creator is Martin Frank is still developing it, so I'd contact him directly for examples.
However there are simpler things like Xiao suggested that can be automated using bash scripts that call cpptraj and gnuplot. By automated I mean you write the scripts once and can regenerate the plots instantly. The scripts are specific to each project though.
Thanks for answering my question. The extra character threw me off and I couldn't find the residue in the prep files. I know there's a Glycam Naming page (http://glycam.org/docs/forcefield/glycam-naming-2/) which I refer to regularly. Could the fourth character information be put on that page? I know it now but I think it'd be helpful for others. Of course if it's already somewhere else please let me know.
These residues have the same prep file. For example, 4uA1, 4uA2, and 4uA3 use the same prep file, 4uA. As David mentioned in the last email, the last character indicates different conformations, but still the same residue.
Best regards,
Xiao
Xiaocong Wang Complex Carbohydrate Research Center The University of Georgia 315 Riverbend Road, Athens, GA, 30602 Tel: (706) 254-7958 E-mail: [log in to unmask]
On Wed, Dec 20, 2017 at 10:03 AM, Xiaocong Wang <[log in to unmask]> wrote:
> Hi Laura, > > > These residues have the same prep file. For example, 4uA1, 4uA2, and 4uA3 > use the same prep file, 4uA. As David mentioned in the last email, the > last character indicates different conformations, but still the same > residue. > > > Best regards, > > > Xiao > > > Xiaocong Wang > Complex
Thanks for the confirmation and information. The information about 4 letter codes on the web site is really helpful. Maybe it'll cut down the number of questions you get. Then again, maybe you'll just end up referring people to the page.
Regards,
Laura
On 12/20/2017 10:19 AM, Lachele Foley wrote: > I have added a section on alternate residue codes/names. Please let me > know if it would be useful to say something more or something different. > > http://glycam.org/docs/forcefield/glycam-naming-2/ > > > On Wed, Dec 20, 2017 at 10:03 AM, Xiaocong Wang <[log in to unmask] > >
The fourth character is simply a placeholder that differentiates the ring conformations that are built. There are currently three that are used (4uA1/4uA2/4uA3) that build the 1C4, 2So, and 4C1 conformations (not necessarily in that order). This is currently only performed for IdoA due to the flexibility of the ring compared to other monosaccharides.
We don't have charge sets for these two sugars yet. I will make a note, and derive charges for them in the future.
Best regards,
Xiao
Xiaocong Wang Complex Carbohydrate Research Center The University of Georgia 315 Riverbend Road, Athens, GA, 30602 Tel: (706) 254-7958 E-mail: [log in to unmask]
From: Users of GLYCAM & GLYCAM-Web [mailto:[log in to unmask]] On Behalf Of Xiaocong Wang Sent: Friday, 15 December 2017 12:13 PM To: [log in to unmask] Subject: Re: β-(1->4)-linked D-mannuronic acid (M)
Hi Neha,
We don't have charge sets for these two sugars yet. I will make a note, and derive charges for them in the future.
