It seems atoms, not molecules... :) ~Vitaly
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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