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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
>>>
>>
>>
>