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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