Dear users, I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex
I¹ve tried to get grompp to work, but I keep getting the following message: _______________________________________________________ >> creating statusfile for 1 node... >> >> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# >> checking input for internal consistency... >> calling /usr/bin/cpp... >> processing topology... >> Generated 165 of the 1596 non-bonded parameter combinations >> Excluding 3 bonded neighbours for Protein 1 >> Excluding 3 bonded neighbours for IN4 1 >> Excluding 2 bonded neighbours for SOL 8756 >> NOTE: >> System has non-zero total charge: 7.999998e+00 >> >> processing coordinates... >> >> ------------------------------------------------------- >> Program grompp, VERSION 3.3.2 >> Source code file: grompp.c, line: 448 >> >> Fatal error: >> number of coordinates in coordinate file (trp_b4ion.pdb, 28394) >> does not match topology (trp.top, 28402) >> ------------------------------------------------------- >> It appears because grompp is ³excluding² the bonded neighbors is what¹s making me end up with the different number of coordinates in my coordinate and topology files. Could anyone please make a suggestion how to fix this fatal error? Below is my .mdp file that is right out of the tutorial. Thanks so very much... I'm almost there!!!!!!!! Dean -- Dr. Dean Cuebas, Associate Prof of Chemistry [email protected], Ph 417-836-8567 FAX 417-836-5507 Dept. of Chemistry, Missouri State University Springfield, Missouri 65897 ; ; mdp input file ; generated by GUIMACS ; ; ; Preprocessing Parameters ; title = Yo cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none ; ; Run Control Parameters ; integrator = steep tinit = 0 dt = 0.002 nsteps = 500 ; ; Energy Minimization Parameters ; emtol = 1000 emstep = 0.01 ; ; Neighbor Searching Parameters ; nstlist = 10 ns_type = grid rlist = 1.0 ; ; Electrostatics Parameters ; coulomb_type = PME rcoulomb = 1.0 ; ; VdW Parameters ; rvdw = 1.4 ; ; Ewald Parameters ; fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes _______________________________________________ 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
