[gmx-users] doubts on g_confrms output

Kwee Hong jestan1985 at yahoo.com
Fri Feb 11 17:45:04 CET 2011

Hi Mark,

I tried but with this error:

Fatal 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: 
Hi Tsjerk,
>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
>Hi Joyce,
>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 
>>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 
>>Herein, I attached part of the pdb file                             generated by 
>>fit_wet.pdb. Any insight is                             welcomed.
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