[gmx-users] doubts on g_confrms output

[David van der Spoel]

On 2011-02-12 02.19, Mark Abraham wrote:
> 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
>>>>

If e.g. 1OMB.pdb does not have hydrogen and md.gro does, you need to 
specify two index files, pointint to e.g. the C-alpha atoms. Then the 
fit can be done on these and your superposition will be fine.


>>>> 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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>>>
>>
>>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se