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.
Charge groups are covered in the manual. See there for details. Since GROMACS evaluates non-bonded energies as sums over charge groups, not sums over atoms, it is not possible to have an energy group that is not a union of whole charge groups. You could re-define the charge groups in the topology (see chapter 5 of the manual) if you were prepared to have more noise as atoms move in and out of the cutoffs, which might be acceptable in a mdrun -rerun context. Still, I'd suggest strongly that you consider what you expect such an analysis to tell you. Protein-ligand interactions are very unlikely to be decomposable into pairwise-additive terms that are a function of subsets of coordinates - especially enzymes. > I am a jackeroo and want to get your advice. Many thanks! Somehow, I doubt it! See http://www.jjoz.com.au/jackjill.htm :-) Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
