VMD-L Mailing List
From: Peter Freddolino (petefred_at_umich.edu)
Date: Sun Dec 11 2016 - 14:46:51 CST
An example would be useful in helping to pin this down. I’d be concerned that some of your atom names don’t match between the input pdb and topology file.
> On Dec 8, 2016, at 10:10 PM, Harish Srinivasan <harishlglk1992_at_gmail.com> wrote:
> 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 autoPSF).
> 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 coordinates.
> Thank you,
> PS : VMD shows warning in the terminal : 'unable to set coordinates for molecule x' while running AutoPSF.