From: Stephani Macalino (
Date: Tue Oct 09 2018 - 02:08:30 CDT

I want to do MD for an induced fit docking (IFD) complex I got from Maestro
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!