[gmx-users] Fatal error: atoms 970 and 973 in charge group 600 are in different energy groups

[Mao-Cai Yan]

Dear colleague,

I want to calculate the  Coul-SR energy and LJ energy between the receptor and PART of my ligand, using a given XTC file with "mdrun -rerun". I modified "energygrps" in the MDP file, and then type

grompp -f md_rerun.mdp -c pr_out.gro -p receptor.top -n index.ndx -o rerun.tpr

Here is the wrong information:


creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 1284 of the 1485 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
turning all bonds into constraints...
Excluding 3 bonded neighbours for AHE 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 8605
turning all bonds into constraints...
Excluding 1 bonded neighbours for Cl 1
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
#     ANGLES:   6004
#      PDIHS:   2890
#      IDIHS:   2400
#       LJ14:   5595
#     CONSTR:   3078
#     SETTLE:   17210
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Not using any simulated annealing
Making dummy/rest group for Acceleration containing 26823 elements
Making dummy/rest group for Freeze containing 26823 elements
Making dummy/rest group for Energy Mon. containing 25851 elements
Making dummy/rest group for VCM containing 26823 elements
Number of degrees of freedom in T-Coupling group Protein is 1882.89
Number of degrees of freedom in T-Coupling group AHE is 111.99
Number of degrees of freedom in T-Coupling group SOL is 51627.11
Number of degrees of freedom in T-Coupling group Cl is 3.00
Making dummy/rest group for User1 containing 26823 elements
Making dummy/rest group for User2 containing 26823 elements
Making dummy/rest group for XTC containing 26823 elements
Making dummy/rest group for Or. Res. Fit containing 26823 elements
T-Coupling       has 4 element(s): Protein AHE SOL Cl
Energy Mon.      has 3 element(s): Protein disaccharide rest
Acceleration     has 1 element(s): rest
Freeze           has 1 element(s): rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 1 element(s): rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
Checking consistency between energy and charge groups...
Fatal error: atoms 970 and 973 in charge group 600 are in different energy groups


I am not sure what "charge group 600" means. Atoms 970 and 973 are in my ligand; atom 970 is in the part of ligand that I want to calculate energy (that is, "disaccharide" in "Energy Mon."), but atom 973 is not.

I am a jackeroo and want to get your advice. Many thanks!


Sincerely,

MC Yan
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