From: Harish Srinivasan (
Date: Thu Dec 08 2016 - 21:10:50 CST

I have been using AutoPSF to generate the structure file (psf) from pdb and
rtf files of the molecules. This successfully generates the psf file but in
every case it fails to set the right coordinates in pdb file (generated by

 Although, I had started using the psf file with my old pdb file as the
structure generated seemed to be intact with the old pdb, it still bothers
me as to why auto generated pdb file doesn't have the right structure and

Thank you,

PS : VMD shows warning in the terminal : 'unable to set coordinates for
molecule x' while running AutoPSF.