[gmx-users] Error in pdb2gmx

[David van der Spoel]

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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