[gmx-users] regarding generation of a topology file using Topolbuild

Bruce D. Ray bray at iupui.edu
Thu Oct 9 14:10:37 CEST 2014

>On Thu, 9 Oct 2014 at 3:00 PM, Sahithya S Iyer <sah2714 at gmail.com> wrote:
>Hello users
>I am trying to generate a topology for CHL (chlorophyll a) using oplsaa ff. I
>am using topolbuild1_3 as an automated tool suggested in the Protein-Ligand
>Tutorial by Justin A. Lemkul to generate topology using oplsaa ff.
>I have converted the pdb file of Chl a to mol2 file ( both of the files
>attached herein). On running the mol2 file, it gives the following error -
>Fatal error.
>Source code file: readmol2.c, line: 765
>Atom 3 (CHB) has 2 connections when required to have 3
>Can you please guide me as to how this error can be rectified ?
>Thanks in advance.

The attachment was not passed on.

Topolbuild tries to check for consistent chemistry because the rules
for selecting atom types will fail if the mol2 atom types are not
consistent with the bonding structure given in the mol2 file.
The error message means that atom number 3 does not have enough bonds
to it for the atom type specified in the mol2 file.  This means there
is an error in how the mol2 file was generated.  There may be more
errors in the mol2 file beyond atom 3 because that error was so severe.
I usually use either Chimera or Avogadro to save mol2 files, but with
these, the type of the guanidino carbon of arginine needs to be
changed to C.cat to meet the Sybyl mol2 specifications.


Bruce D. Ray, Ph.D.
Associate Scientist
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202-3273

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