From: Fotis Baltoumas (
Date: Tue Oct 09 2018 - 05:18:14 CDT


When dealing with non-protein or non-nucleic acid molecules, psfgen
NEEDS the atom coordinates to match the provided topology exactly.

Make sure that the naming scheme AND atom order in your ligand's PDB
file and the naming scheme in the topology file generated by swiss-param
are the same.  Also, make sure the residue name is the same (I can't be
sure but I think swiss-param often renames the molecule to "LIG" or

Also, make sure that the pdb file you submit to psfgen has ALL its atoms
(hydrogens etc).

Good luck,


On 10/09/2018 10:08 AM, Stephani Macalino wrote:
> Hello,
> I want to do MD for an induced fit docking (IFD) complex I got from
> Maestro Schrodinger.
> I got ligand parameter files from swiss param and tried to use VMD and
> Solvate to make a waterbox around my complex.
> However, when I do the psfgen, it always shows "Warning: failed to set
> coordinate for atom XX RES:##"
> Then the psf file that I get is empty since every atom has no
> coordinates. I don't understand why this is happening.
> I already finished 100 ns MD run for WT and mutants of the same
> protein following the same procedure for solvation (except for ligand
> topology).
> Hope you can help me. Thank you!
> Regards,
> Stephani

Fotis A. Baltoumas
Bioinformatics Postgraduate Programme
Section of Cell Biology and Biophysics
Department of Biology, National & Kapodistrian University of Athens
Panepistimiopolis, Athens 157 01, GREECE
email :