[gmx-users] doubts on g_confrms output

Kwee Hong jestan1985 at yahoo.com
Fri Feb 11 16:55:27 CET 2011

Hi Tsjerk,

Thanks for the help. I got it.
But do you have any idea how to solve this in vmd?


From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, January 22, 2011 15:53:22
Subject: Re: [gmx-users] doubts on g_confrms output

Hi Joyce,
In pymol use 'set all_states'
On Jan 22, 2011 8:30 AM, "Kwee Hong" <jestan1985 at yahoo.com> wrote:
>I was trying to do some analysis following John's "GROMACS tutorial for 
>solvation study of spider toxin peptide".
>I'm using GROMACS-4.5.3 and my command line for g_confrms is 
>g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb
>The program calculated the RMSD sucessfully and fit_wet.pdb was generated. Yet, 
>when i tried to visualise fit_wet.pdb using VMD, the structure is obviously in a 
>mess. And when I tried it out  with pymol, I can only visualised one model. 
>Model 2 did not appear. I wonder would it be the pdb format generated by 
>g_confrms is not the standard pdb format and had caused VMD and final failed to 
>read  them?
>Herein, I attached part of the pdb file generated by  fit_wet.pdb. Any insight 
>is welcomed.
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