[gmx-users] Error in pdb2gmx

[David van der Spoel]

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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