submit a bug report at bugzilla.gromacs.org?
On 10/17/2007 2:40 AM, Justin A. Lemkul wrote:
Hello all,
I am having a strange error when using pdb2gmx. I am trying to generate the
topology for a simple protein, using Gromos96 43a1. I am able to create the
topology with version 3.3 without issue. However, if I use pdb2gmx under
version 3.3.1, I encounter this:
$ pdb2gmx -f protein.pdb -o protein.gro -ignh
(pdb2gmx runs through its normal routine...)
-------------------------------------------------
Program pdb2gmx, VERSION 3.3.1
Source code file: pgutil.c, line: 87
Fatal error:
Atom N not found in residue 1 while adding improper
-------------------------------------------------
If I try the ffgmx force field, everything works fine. There are no broken
residues in the PDB (it's one that I've worked with before, just with a
different force field).
I have not tried to generate the topology under version 3.3.2, because our
university's cluster only has versions 3.3 and 3.3.1 available. I suppose I
can just use version 3.3, but I thought I should bring up this issue in case it
needs fixing in future versions (or in case I'm missing something that should be
an easy fix).
-Justin
======================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/
======================
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