<div dir="ltr">Hi david,<br>Thanx again, but I want to ask what changes need to be done there in such cases.<br><br>With Thanx,<br>Vivek<br><br><div class="gmail_quote">2008/8/12 David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">vivek sharma wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi David,<br>
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.<br>
</blockquote>
<br></div>
with a text editor, like emacs, notepad or whatever.<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
With Thanx,<br>
Vivek<br>
<br>
2008/8/12 David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>><div><div>
</div><div class="Wj3C7c"><br>
<br>
vivek sharma wrote:<br>
<br>
Hello there,<br>
I am trying to run pdb2gmx on 3bzu.pdb file and got the<br>
following error<br>
<br>
Opening library file /usr/share/gromacs/top/<br>
ffG43b1.rtp<br>
Opening library file /usr/share/gromacs/top/aminoacids.dat<br>
Reading 3bzu.pdb...<br>
WARNING: all CONECT records are ignored<br>
Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6<br>
BETA-HSD1', 8581 atoms<br>
Opening library file /usr/share/gromacs/top/xlateat.dat<br>
26 out of 26 lines of xlateat.dat converted succesfully<br>
Analyzing pdb file<br>
<br>
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 3.3.3<br>
Source code file: pdb2gmx.c, line: 878<br>
<br>
Fatal error:<br>
Chain identifier 'A' was used in two non-sequential blocks<br>
(residue 1034, atom 7961)<br>
-------------------------------------------------------<br>
as I am new to this field. I'm finding it very difficult to<br>
find the reason and rectify it.<br>
Any suggestion would be of great help......<br>
<br>
This is a limitation in pdb2gmx. It expects the atoms in the chain<br>
A to be in sequence in the pdb file. You can manually sort the pdb<br>
file on the chain identifier.<br>
<br>
<br>
With Thanx,<br>
Vivek<br>
------------------------------------------------------------------------<br>
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