> > > I am running simulation for the drug enzyme complex using Gromacs with > gromacs96(43a2)forcefield. After generating waterbox around my protein, > when I am running grompp command (before energy minimization) I am getting > following error: > > --------------------------------------------------------------------------- > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# > checking input for internal consistency... > calling /lib/cpp... > processing topology... > Generated 380 of the 1326 non-bonded parameter combinations > Excluding 3 bonded neighbours for Protein_A 1 > Excluding 2 bonded neighbours for SOL 735 > Excluding 3 bonded neighbours for ZPR 1 > Excluding 2 bonded neighbours for SOL 36755 > NOTE: > System has non-zero total charge: -1.999999e+01 > > processing coordinates... > -------------------------------------------------------------------------- > Program grompp_mpi, VERSION 3.3.1 > Source code file: grompp.c, line: 448 > > Fatal error: > number of coordinates in coordinate file (protein_gen.pdb, 119825) > does not match topology (topology.top, 119830) > -------------------------------------------------------------------------- > > I checked gromacs wiki page > also( > http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology > ) > but not able to solve this error.I am getting this error before adding > ions. > > Can anybody help me regarding same and suggest what could be possible > reason for this ? > > Thanks, > > Regards, >
I guess you just missed five atoms in your gro file. Does the number of solvent molecules in the coordinate file equal to that in the topology? ~ Vitaly -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: [email protected],[email protected] skype: vvchaban, mob.: +38-097-8259698
_______________________________________________ gmx-users mailing list [email protected] http://lists.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
