Re: [AMBER] tleap using GLYCAM force field

From: Lachele Foley <>
Date: Mon, 23 Jun 2014 11:32:51 -0400

You can't (yet) build cyclic structures using GLYCAM-Web. You can
build it using your pdb file, but you'll have to modify it first. I'm
surprised you got anything at all from it as-is.

1. Remove all lines from the PDB file that do not begin with "HETATM" or "END".

2. Change all the residue names from GLC to 4GA.

3. Change these atom names: H62 and H63 to H61 and H62; HO2, HO3 and
HO6 to H2O, H3O and H6O.

4. Add TER cards between each of the residues.

5. Use the following, or something equivalent, as input to tleap.
This assumes you call your new pdb file "rec_modified.pdb".

source leaprc.GLYCAM_06j-1

m = loadpdb rec_modified.pdb

bond m.901.C1 m.902.O4
bond m.902.C1 m.903.O4
bond m.903.C1 m.904.O4
bond m.904.C1 m.905.O4
bond m.905.C1 m.906.O4
bond m.906.C1 m.907.O4
bond m.907.C1 m.908.O4
bond m.908.C1 m.901.O4

check m

saveamberparm m m.parm7 m.rst7

On Mon, Jun 23, 2014 at 8:00 AM, Shreeramesh <> wrote:
> Hi
> I am working on the binding free energy calculation for
> gammacyclodextrin-ligand complex using GLYCAM forcefield
> I represented the residues of carbohydrates as 4GA in my pdb file which
> comprises 8 glucose unit
> While running tleap, it saves only one residues of glucose with ligand in
> solvated complex. It omits the remaining seven residues
> I also attached the .pdb file. Can anybody guide for getting the solvated
> complex with 8 sugar unit of gammacyclodextrin-ligand in tleap using GLYCAM
> force field.
> Thanks
> Ramesh
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Mon Jun 23 2014 - 09:00:02 PDT
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