[gmx-users] doubts on g_confrms output
jestan1985 at yahoo.com
Fri Feb 11 17:45:04 CET 2011
I tried but with this error:
Number of atoms in pdb frame 0 is 331 instead of 491
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, February 12, 2011 0:01:39
Subject: Re: [gmx-users] doubts on g_confrms output
On 12/02/2011 2:55 AM, Kwee Hong wrote:
>Thanks for the help. I got it.
>But do you have any idea how to solve this in vmd?
Use trjconv -sep on the .pdb file to split it.
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>
>>I was trying to do some analysis following John's
>>"GROMACS tutorial for solvation study of spider
>>I'm using GROMACS-4.5.3 and my command line for
>>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
>>Herein, I attached part of the pdb file generated by
>>fit_wet.pdb. Any insight is welcomed.
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