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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 >> > >