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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
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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