[gmx-users] error: T-coupling groups

vema aparna vemaparna at rediffmail.com
Fri Jan 21 07:49:13 CET 2005

Hello Gromacs users,

I am running MD for a protein with its crystal water. I have again solvated the system using genbox. Thus the topology file contains 4 groups under the division molecule as


protein_A       1
Ligand          1
SOL             150
SOL            32459

When i go for preprocessing the system for MD, i got an error

Fatal error: atom no.2015 in more than one T-coupling groups (14 and 2)

i checked the gro file to find that atom 2015 corresponds to last atom of the ligand.

I checked the index file. it has no error. 
So i have given the index  file as an input and rerun the grompp command.

This time i got an error

FATAL error: atom 2469 in more than one T-coupling groups(15 and 2)

and this atom corresponds to the last atom of the SOL (crystal water) group.
I have also checked the index file to find no error in grouping this atom.

Can anyone suggest me how can i get rid of this problem

Thanking you in advance


Vema Aparna
Prof. G. R. Desiraju's Group,
School of Chemistry
University of Hyderabad
Hyderabad - 500 046
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