Print

Print


Hello Oliver,

Many thanks for your reply. The disaccharide unit I used to build heparin
is,  2-O-sulfo-alpha-L-iduronic acid (LIdopA[2S]a) 1->4 linked to
2-deoxy-2-sulfamido-alpha-D-glucopyranosyl-6-O-sulfate (DGlcpNS[6S]a). The
heparin I build have two of this disaccharide unit linked together. Each
disaccharide unit have one carboxyl and three sulfate attached ( carboxyl
and one sulfate attached to iduronic acid, and two sulfate attached to 2nd
and 6th position of glucopyranosyl moiety). Thus carry a total of -8 charge.

The GAG builder generated structure have deprotonated carboxyl group, thus
carry a -ve charge on carboxyl group as well.

Please correct me if I am wrong here.

Thanks
Anu

On Wed, Nov 18, 2015 at 12:26 PM, Oliver Grant <[log in to unmask]>
wrote:

> Hi Anu,
>
> Each of your sulfate and iduronic acid residues carry a net -1 charge,
> making the total charge on your GAG -6. I need more information on why you
> want it to be -8 before I can advise you. The sequence you showed above
> would not have a -8 charge. It could be that the sequence you require has a
> sulfate at both the 6 and 3 position of the GlcNAc (as occurs in "heparin")
> e.g. DGlcpNAc[3S,6S]a1-4LIdopA[2S]a1-4DGlcpNAc[3S,6S]a1-4LIdopA[2S]a1-OME
> This would have a -8 charge.
>
>
> Oliver
>
> On Tue, Nov 17, 2015 at 8:03 PM, Oliver Grant <[log in to unmask]>
> wrote:
>
>> LINK cards can be ignored.
>>
>>
>> Yes that is what TER cards will do in tleap.
>>
>>
>> Tleap was designed for proteins and thus assumes a linear sequence of
>> residues. It will bond the tail atom of a residue to the head atom of the
>> next residue unless you place a TER card between them. Your molecule is
>> technically branched as you have sulfate residues attached. Best is to add
>> TER cards between EVERY residue and explicitly bond them with tleap bond
>> commands. If you separate the LINK cards into a separate file, you may run
>> the attached LINK2bond on it to produce tleap bond commands. Just chmod +x
>> LINK2bond once you download it.
>> We also find all this overly complex! It will soon be a thing of the past.
>> On 17 Nov 2015 5:27 p.m., "anu chandra" <[log in to unmask]> wrote:
>>
>>> Thanks to all for your helpful reply.
>>>
>>> As a beginner, I build the heparin unit - LIdopA[2S]a1-4DGlcpNS[6S]a1-4LIdopA[2S]a1-4DGlcpNS[6S]a1-OH
>>> - using GAG builder in order get familiarize with the Glycam naming, before
>>> renaming the heparin pdb file I have.
>>>
>>> Here, I am little confused with the format of the generated pdb file. I
>>> have noticed that top of the pdb file have  following details mentioned,
>>>
>>> LINK         O1  ROH     1                 C1  UYS     2
>>> LINK         O6  UYS     2                 S1  SO3     9
>>> LINK         O4  UYS     2                 C1  YuA     3
>>> LINK         O4  YuA     3                 C1  UYS     4
>>> LINK         O2  YuA     3                 S1  SO3     8
>>> LINK         O6  UYS     4                 S1  SO3     7
>>> LINK         O4  UYS     4                 C1  2uA     5
>>> LINK         O2  2uA     5                 S1  SO3     6
>>>
>>> Is this just for the information or do I need to keep this information
>>> in my pdb file as well?
>>>
>>>
>>> I have also noticed that there is a TER card in between the
>>> monosaccharide units in amber formatted pdb file (1_AMBER.pdb). For e.g.,
>>>
>>> HETATM   25  O5  UYS     2       8.455   8.107  -2.556  1.00
>>> 0.00           O
>>> HETATM   26  O4  UYS     2       8.472   7.396  -6.246  1.00
>>> 0.00           O
>>> TER
>>> HETATM   27  C1  YuA     3       9.694   7.499  -7.062  1.00
>>> 0.00           C
>>> HETATM   28  H1  YuA     3      10.522   7.063  -6.507  1.00
>>> 0.00           H
>>>
>>> If I am right, usually  TER card is placed only when a residue get
>>> terminated ( i.e not bonded to the next residue). May I know why TER card
>>> is inserted in between the covalently linked monosccharide units?
>>>
>>>
>>> Also, how do I re-adjust the atomic charges if I need to  set the total
>>> charge on heparin to 8 -ve?
>>>
>>>
>>> Many thanks once again
>>> Anu
>>>
>>>
>>> On Tue, Nov 17, 2015 at 2:12 PM, Oliver Grant <[log in to unmask]>
>>> wrote:
>>>
>>>> Hi Anu,
>>>>
>>>> No you won't have to do that. When connecting sulfates you just adjust
>>>> the charge on the connecting oxygen/nitrogen in tleap. E.g:
>>>> set mol.160.O6 charge -0.437
>>>> I adjusted it by + 0.031. Replace mol.160 as appropriate for your
>>>> system.
>>>> For attaching a sulfate to the N of a b-GlcN you need to adjust the
>>>> charge on the linking N by -0.057. You can find out what charge the N
>>>> is in tleap with e.g:
>>>> charge mol.3.N2
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Oliver
>>>>
>>>> On Tue, Nov 17, 2015 at 2:28 PM, anu chandra <[log in to unmask]>
>>>> wrote:
>>>>
>>>>> Hi Oliver,
>>>>>
>>>>>
>>>>> Thanks for your prompt reply. A quick query here is about the RESP
>>>>> charge calculation. I have noticed that in Glycam, the atomic partial
>>>>> charges are derived for monosaccharide units and also mentioned about
>>>>> change in charge while adding functional groups like sulfates. Do I need to
>>>>> do any  geometry optimization and partial charge calculation for the
>>>>> heparin I am using?. The heparin contains two disaccharide units.
>>>>>
>>>>>
>>>>> Many thanks
>>>>>
>>>>> Anu
>>>>>
>>>>> On Mon, Nov 16, 2015 at 6:40 PM, Oliver Grant <[log in to unmask]>
>>>>> wrote:
>>>>>
>>>>>> Hi Anu,
>>>>>>
>>>>>> I forgot about adding sulfates. You'll also have to follow this page:
>>>>>>
>>>>>> http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/
>>>>>>
>>>>>> Oliver
>>>>>>
>>>>>> On Mon, Nov 16, 2015 at 6:12 PM, Oliver Grant <[log in to unmask]
>>>>>> > wrote:
>>>>>>
>>>>>>> Hi Anu,
>>>>>>>
>>>>>>> I think this is the standard protocol right now:
>>>>>>>
>>>>>>> Add these lines to your tleap input file. Insert your own paths and
>>>>>>> forcefields that you are using.
>>>>>>>
>>>>>>> source /programs/amber/dat/leap/cmd/leaprc.GLYCAM_06j-1
>>>>>>> source /programs/amber/dat/leap/cmd/leaprc.ff14SB
>>>>>>>
>>>>>>> You can see I'm using AMBER14. Now the hard part is getting your
>>>>>>> ligand named correctly so that the correct GLYCAM parameters get assigned
>>>>>>> when you load it into tleap. Protein residues have standard names in the
>>>>>>> PDB, but unfortunately carbs do not. I assume you have a PDB format file of
>>>>>>> the co-complex. You have to manually edit the PDB file with a text editor,
>>>>>>> renaming the residues and atom names to GLYCAM nomenclature. See here for
>>>>>>> the nomenclature to use:
>>>>>>> http://glycam.org/docs/forcefield/glycam-naming-2/
>>>>>>> If this is your first time, it will be useful for you to build the
>>>>>>> sugar on our website, download the PDB file, and open it up in a text
>>>>>>> editor. You will see what format the carbohydrate residues and atom names
>>>>>>> need to be in. Arunima Singh and others from the group have made a GAG
>>>>>>> builder for this:
>>>>>>> http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=8.
>>>>>>> Write back if you have any trouble with it. User feedback is precious to us.
>>>>>>>
>>>>>>> In the very near future (we are testing the software right now)
>>>>>>> we'll be releasing software that renames everything for you, so this will
>>>>>>> be so much easier.
>>>>>>>
>>>>>>> All the best,
>>>>>>>
>>>>>>> Oliver
>>>>>>>
>>>>>>> On Mon, Nov 16, 2015 at 3:35 PM, SUBSCRIBE GLYCAM-L Anu <
>>>>>>> [log in to unmask]> wrote:
>>>>>>>
>>>>>>>> Hello Glycam users,
>>>>>>>>
>>>>>>>> I am planning to do MD simulation of a protein-ligand complex in
>>>>>>>> which ligand is heparin, made of 2-O-sulfo-aplha-L-iduronic acid and
>>>>>>>> 2-deoxy-2-sulamido-alpha-D-glucopyranosyl-6-O-sulfate. I am using Amber 12
>>>>>>>> MD package for simulation. It will be of great help if somebody can help me
>>>>>>>> to get the Amber compatible Glycam  parameters for heparin.
>>>>>>>>
>>>>>>>>
>>>>>>>> Many thanks
>>>>>>>> Anu
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>