VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Apr 06 2017 - 19:06:36 CDT

Dear Harish,

the issue seems to be on the names of the hydrogen atoms. If you change the
names both in topology and pdb files as H<carbon index><hydrogen index> it
will fix the issue (e.g. second hydrogen of the carbon C1- H12).

By the way, is this topology different from the topology on the
topopar/stream/lipid/toppar_all36_lipid_detergent.str file (CHARMM36
folder)?

Best

Joao
On Thu, Apr 6, 2017 at 1:42 AM Harish Srinivasan <harishlglk1992_at_gmail.com>
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 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
jribeiro_at_ks.uiuc.edu
+1 (217) 3000380