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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
>>>>>
>>>>
>>>>
>>>
>>
>