[gmx-users] Error in pdb2gmx

[vivek sharma]

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 Thanx,
Vivek

2008/8/12 David van der Spoel <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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>
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