[gmx-users] doubts on g_confrms output
jestan1985 at yahoo.com
Fri Feb 11 16:55:27 CET 2011
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
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
>Herein, I attached part of the pdb file generated by fit_wet.pdb. Any insight
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