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:
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
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

All the best,


On Mon, Nov 16, 2015 at 3:35 PM, SUBSCRIBE GLYCAM-L Anu <[log in to unmask]>

> 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