From: Peter Freddolino (
Date: Thu Apr 06 2017 - 19:50:01 CDT

Dear Harish,
Could you please confirm the version of vmd that you are using, and the set of topology files that you have loaded? When I use your inputs with autopsf it gives correct output.

> On Apr 6, 2017, at 2:37 AM, Harish Srinivasan <> wrote:
> Hi,
> I am trying to construct a psf file from a given pdb file. I am using an rtf file for topology of the molecule. After the generating psf file, the autopdb file generated has a really messed up structure.
> I have attached the initial pdb & rtf files and the final generated autopdb and autopsf files here.
> What could be the reason behind this ?
> Thank you
> Harish
> <dodecylsulphate.rtf><dodecylsulphate2.pdb><dodecylsulphate2_autopsf.psf><dodecylsulphate2_autopsf.pdb>