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

[Yang Ye]

you shall check what this warning message claims first.

Mao-Cai Yan wrote:
> 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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