[gmx-users] Error in pdb2gmx

[Justin A. Lemkul]

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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