[gmx-users] Constructing covalent bond between protein-ligand complex

Suman Nandy nandy.suman at rediffmail.com
Fri Jan 13 12:22:27 CET 2012

Dear all,
Guided by gmxusers' list I have used gmx_top_tools.tgz (http://www.gromacs.org/Downloads/User_contributions/Other_software) to prepare the protein-ligand complex linked by a covalent bond. Unfortunately the tool "renumtop" is detecting a duplicate atom but not updating its number. Only gives an error message:
; ERROR: duplicate atom label '4968' for atom #4968 (already used for atom #4968)

I used the command "./renumtop topol_Protein_chain_A.itp topol_Chain_B.itp". may be I am doing something wrong. Please help.

Suman Nandy

Suman Kumar Nandy
Senior Research Fellow
Department of Biochemistry & Biophysics
University of Kalyani
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