[gmx-users] Problem with using topolbuild1_3.tgz

Bruce D. Ray brucedray at yahoo.com
Fri Jan 21 15:55:30 CET 2011

On Thu, January 20, 2011 at 6:41PM, Sweta Iyer <iyer at wehi.EDU.AU> wrote:
> Hi, I am trying to generate topology files for a set of lipids with the
> help of topolbuild1_3.tgz package found at the other software page of
> GROMACS website.
> I downloaded and installed all files and tried running the program with a
> MOL2 file with charges in it. However, it shows an error message as
> follows:
> Fatal error.
> Source code file: readmol2.c, line: 758
> Atom 1 (C) has 3 connections when allowed 0
> I am not sure how to get over this problem! Wonder what will fix this
> error and get the program running!
A major requirement of topolbuild is that the mol2 file use correct atom
types as defined by Tripos, whose file format mol2 is, and as used in Sybyl.
The error message suggests that you have not specified correct Tripos Sybyl
atom types.  There may be other problems in your mol2 file as well.
Correct the atom types and check that the file is otherwise syntactically
correct and it should work.

However, I believe that lipid topology files for gromacs are already available
for download.

I hope that helps.

Bruce D. Ray, Ph.D.
Associate Scientist
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273

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