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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