[gmx-users] doubts on g_confrms output

[Mark Abraham]

On 12/02/2011 3:45 AM, Kwee Hong wrote:
> Hi Mark,
>
> I tried but with this error:
>
> Fatal error:
> Number of atoms in pdb frame 0 is 331 instead of 491

OK. I don't know why two frames with different numbers of atoms are 
written. Maybe g_confrms -one is useful. Or you can chop apart the PDB 
by hand in a text editor.

Mark

> ------------------------------------------------------------------------
> *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.
>
> Mark
>
>>
>> Regards,
>> Joyce
>>
>> ------------------------------------------------------------------------
>> *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'
>>
>> Cheers,
>>
>> Tsjerk
>>
>>> On Jan 22, 2011 8:30 AM, "Kwee Hong" <jestan1985 at yahoo.com 
>>> <mailto:jestan1985 at yahoo.com>> wrote:
>>>
>>> Hi,
>>>
>>> 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.
>>>
>>> Thanks,
>>> Joyce
>>>
>>>
>>>
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>>
>
>

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