[gmx-users] Error in pdb2gmx

[vivek sharma]

Hi david,
Thanx again, but I want to ask what changes need to be done there in such
cases.

With Thanx,
Vivek

2008/8/12 David van der Spoel <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>>
>>
>>
>>    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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