By hand is the easiest way.
> > > Ya, sorry I wrote it wrong.But why these extra atoms are present in my > topology file and how to correct it. > > Thanks, > > Regards, > Swati > > > > > On Thu, Jul 16, 2009 at 12:36 PM, <[email protected]> wrote: > > > >> Hi, > >> > >> thanks for your reply. > >> > >> Yes their is difference of 5 solvent molecules. They are more in number > >> in > >> my topology file. > >> > >> Regards, > >> Swati > >> > >> >> > >> >> > >> >> 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 > >> >
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