[gmx-users] Error in pdb2gmx

Tue Aug 12 16:59:47 CEST 2008

Well,

sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
file.pdb | sort | cut -b 2- > sorted.pdb

sort of seems to do the trick. But it will place the chainless things first.

Hope it helps,

Tsjerk

On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> vivek sharma wrote:
>>
>> Hi david,
>> Thanx again, but I want to ask what changes need to be done there in such
>> cases.
>>
>
> The chain identifier needs to be continuous.  That is, if you have atoms
> with chain identifiers like:
>
> A
> A
> B
> A
> C
> A
> A
>
> they should be re-written as:
>
> A
> A
> A
> A
> A
> B
> C
>
> This can be accomplished with some work in a simple text editor.
>
> -Justin
>
>> With Thanx,
>> Vivek
>>
>> 2008/8/12 David van der Spoel <spoel at xray.bmc.uu.se
>> <mailto:spoel at xray.bmc.uu.se>>
>>
>>    vivek sharma wrote:
>>
>>        Hi David,
>>        Thanks for the quick reply. My apologies for asking you again a
>>        silly doubt as, I am doing this all for the first time. It will
>>        be of great help if you can tell me how to do such correction
>>        manually.
>>
>>
>>    with a text editor, like emacs, notepad or whatever.
>>
>>
>>        With Thanx,
>>        Vivek
>>
>>        2008/8/12 David van der Spoel <spoel at xray.bmc.uu.se
>>        <mailto:spoel at xray.bmc.uu.se> <mailto:spoel at xray.bmc.uu.se
>>        <mailto:spoel at xray.bmc.uu.se>>>
>>
>>
>>           vivek sharma wrote:
>>
>>               Hello there,
>>               I am trying to run pdb2gmx on 3bzu.pdb file and got the
>>               following error
>>
>>               Opening library file /usr/share/gromacs/top/
>>               ffG43b1.rtp
>>               Opening library file /usr/share/gromacs/top/aminoacids.dat
>>               Reading 3bzu.pdb...
>>               WARNING: all CONECT records are ignored
>>               Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6
>>               BETA-HSD1', 8581 atoms
>>               Opening library file /usr/share/gromacs/top/xlateat.dat
>>               26 out of 26 lines of xlateat.dat converted succesfully
>>               Analyzing pdb file
>>
>>               -------------------------------------------------------
>>               Program pdb2gmx, VERSION 3.3.3
>>               Source code file: pdb2gmx.c, line: 878
>>
>>               Fatal error:
>>               Chain identifier 'A' was used in two non-sequential blocks
>>               (residue 1034, atom 7961)
>>               -------------------------------------------------------
>>                as I am new to this field. I'm finding it very difficult to
>>               find the reason and rectify it.
>>               Any suggestion would be of great help......
>>
>>           This is a limitation in pdb2gmx. It expects the atoms in the
>>        chain
>>           A to be in sequence in the pdb file. You can manually sort
>>        the pdb
>>           file on the chain identifier.
>>
>>
>>               With Thanx,
>>               Vivek
>>
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> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623