[gmx-users] pdb2gmx error - version 3.3.1

[Yang Ye]

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
> jalemkul at vt.edu | (540) 231-9080
> http://bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ======================
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