[gmx-users] Regarding atom numbering in .top and .gro files

bipin singh bipinelmat at gmail.com
Sat Sep 28 17:20:03 CEST 2013

Hi all,

I want to put off constraint between some bonds in my system based on their
atom numbers but the .gro file and .top file atom numbers do not match,
because I used .pdb file to generate this .top file using pdb2gmx. (the top
files contains the atom numbers based on this initial input .pdb file and
the subsequent .gro file contains different atom numbering)

I know that grompp generate constraints based on atomtypes in .top file but
If I use the .pdb file (used during pdb2gmx) to do this will it be  fine,
as I will be using this .top file with .gro file for grompp.

Thanks and Regards,
Bipin Singh*

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