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