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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
>>
>
>