[gmx-users] pdb2gmx error - version 3.3.1

[Justin A. Lemkul]

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

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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://bevanlab.biochem.vt.edu/Pages/Personal/justin/

======================