Dear Users, I am trying to simulate Drug - Enzyme Complex accoring to "GROMACS Tutorial for Drug - Enzyme Complex" with different enzyme (ALKALINE PHOSPHATASE FROM HUMAN PLACENTA - ZEF1) and ligand. After adding water with genbox I run:
grompp -f em.mdp -c trp_b4ion.pdb -p trp.top -o trp_b4ion.tpr This is what I got: creating statusfile for 1 node... ' for variable integrator, using 'md' Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi' ' for variable ns-type, using 'Grid' Next time use one of: 'Grid' 'Simple' ' for variable optimize_fft, using 'no' Next time use one of: 'no' 'yes' ' for variable constraints, using 'none' Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 Excluding 3 bonded neighbours for DRG 1 Excluding 2 bonded neighbours for SOL 21179 Excluding 2 bonded neighbours for SOL 1711 NOTE: System has non-zero total charge: -6.999996e+00 processing coordinates... double-checking input for internal consistency... ------------------------------------------------------- Program grompp, VERSION 3.3.1 Source code file: grompp.c, line: 1109 Fatal error: There were 4 error(s) processing your input ------------------------------------------------------- "Working in the Burger Kings, Spitting on your Onion Rings" (Slim Shady) I would like to know what was wrong with the molecules, but there was absolutely no indication of that. Could anyone explain what this 'double-checking' means and how to get something meaningful of it? I have also tried some Windows versions (3.2.1, 3.3). They have also failed, but were able to go beyond this point. Maybe the problem is with Protein_B which consists of Mg and Zn ions. Thank you in advance for your help.
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