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

Sahithya S Iyer sah2714 at gmail.com
Thu Oct 9 11:30:19 CEST 2014

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.

Sahithya S Iyer

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