[gmx-users] doubts on g_confrms output

[Tsjerk Wassenaar]

Hoi :)

Maybe the following lines are useful. First, to extract the first
model from a PDB file:

sed /ENDMDL/q trajectory.pdb > first.pdb

Just for the record, to extract a specific frame # from a PDB file:

sed -ne '{/^MODEL *# /,/ENDMDL/p}' trajectory.pdb > frame-#.pdb (NOTE:
replace # with the number)

Then, to extract the last frame from a PDB file:

sed -ne '/^MODEL/,/^ENDMDL/{/^MODEL/{x;d};H}' -e '${x;p}'
trajectory.pdb > last.pdb

With these lines it  does not matter whether the frames/models have
equal (numbers of) atoms or not.

Hope it helps,

Tsjerk

On Sat, Feb 12, 2011 at 10:09 AM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> 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
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
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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
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands