[gmx-users] remove the atom clashes-reg

ITHAYARAJA ithayaraja at gmail.com
Wed Aug 31 10:15:34 CEST 2011

Hi Dear,

I am doing simulation with three ligand so that I have applied deprecated
force field to the system.

I went through the reference which you cited to the following error. I
understood the error that It could be a clashes. It wanted to  remove atom
clashes from my coordinate file, so Is there any option to do the same. help

Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/toppush.c, line: 947

Fatal error:
Atomtype NR not found

Ithayaraja M,
Research Scholar,
Department of Bionformatics,
Bharathiar University,
Coimbatore 641 046,
Tamil Nadu
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