[gmx-users] error: Atom 1 in multiple Energy Mon. groups

[nazli kashani javid]

Hi all
I want to calculate interaction energy of my protein that includes 4
individual chains(a,b,c and d). at first I define an index file. It
contains:
[ chaina ]
 1    2    3    4 ...454
[ chainb ]
455  456  457 ...919
[ chainc ]
920  921  922 .... 1373
[ chaind ]
1374 1375 1376 ....1838
[ chainsab ]
 1    2    3....919
[ chainsac ]
  1    2    3 ...454    920....1373
[ chainsad ]
......
[ chainsbc ]
.....
[ chainsbd ]
..........
[ chainscd ]
........
[ chainsabc]
1    2    3 .... 1373
[ chainsacd ]
1    2    3 .....454   920 ...1838
[ chainsabd ]
......
[ chainsbcd ]
........

I add these groups to .mdp file as following:

energygrps  =  chaina chainb chainc  chaind chainsab  chainsac chainsad
chainsbc chainsbd chainscd chainsabc chainsacd chainsabd chainsbcd

when I use grompp command ( grompp -f md.mdp -c npt.gro -p topol.top -n
chains.ndx -o mda.tpr)  , and face with this error :

Fatal error:
Atom 1 in multiple Energy Mon. groups (1 and 5)
For more information and tips for troubleshooting, please check the GROMACS


dose my index file need any modifications? is there any wrong with my mdp
file?
how could I solve my problem?

any help  is appreciated.