[gmx-users] ligand protein complex with ffamber99

Ragnarok sdf fabracht1 at gmail.com
Sun Nov 23 16:27:27 CET 2008

I am trying to setup a simulation with a ligand and a protein using
ffamber99 forcefield. I have already generated the ligand's topology file
using acpypi and everything seems to be all right in the files generated.
However, while following the steps in the drug enzyme tutorial provided in
the gromacs' web site, after i add the ligand to my protein's .gro file and
edit the lines in my topology file to include the ligand's topology, when i
type the command editconf, my ligand dissapears from my .gro file. The .gro
generated from my original ligand-protein complex.gro does not include my
ligand coordinates whatsoever.
I've tested this procedure once with a different system using ffgmx
forcefields and everything went all right. However, now that i am using
ffamber99 forcefield everything seems to be working against me. It took me
quite some time to figure out how to generate topology files for ligands
with this forcefield. So I would really aprecciate some help on the matter.
Thank you in advance
Fabrício Bracht
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