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/ ====================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
