[gmx-users] topology and coordinate file not matching after grompp

[Swagata Patra]

Dear Sapna.

After adding benzene molecules also I am getting the same error.

On Tue, Feb 9, 2016 at 10:56 AM, SAPNA BORAH <sapnauser365 at gmail.com> wrote:

> Dear Swagata,
>
> You have to include the benzene molecules in your topology section.
>
> [ molecules ]
>
> ; Compound        #mols
>
> Protein_chain_A     1
>
> PDB               250*6
>
> SOL              7217
>
> BENZENE       xyz
>
>
> It should solve your problem.
>
> Sapna.
>
>
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
>
> On Tue, Feb 9, 2016 at 10:46 AM, Swagata Patra <swagataliza at gmail.com>
> wrote:
>
> > Hi gromacs users.
> >
> >
> >
> > I am trying to simulate a protein is mixed solution of water and 25%
> > benzene using gromos force field.
> >
> > I tried to follow the steps suggested on gromacs website.
> >
> >  Here are the commands that I used:
> >
> >
> >
> > > pdb2gmx_d -f protein.pdb -o protein_processed.gro -water spce -ignh
> >
> > > editconf_d -f protein_processed.gro -o protein_newbox.gro -c -d 1.0 -bt
> > cubic
> >
> > > genbox_d -cp protein_newbox.gro -ci benz.gro -nmol 250 -o phase1.gro (I
> > got the .gro file using prodrg)
> >
> > > genbox_d -cp phase1.gro -cs spc216.gro -o solvated.gro
> >
> >
> >
> > I prepared the .gro and .itp file using PRODRG. As I want to simulate the
> > protein in 25% benzene that’s why I am adding 250 in –ci –nmol option.
> >
> > After getting the solvated.gro file I edited topol.top file
> >
> > ; Include Position restraint file
> >
> > #ifdef POSRES
> >
> > #include "posre.itp"
> >
> > #endif
> >
> >
> >
> > ; Include benzene topology
> >
> > #include "benz.itp"
> >
> >
> >
> > ; Include water topology
> >
> > #include "gromos43a1.ff/spce.itp"
> >
> >
> >
> > #ifdef POSRES_WATER
> >
> > ; Position restraint for each water oxygen
> >
> > [ position_restraints ]
> >
> > ;  i funct       fcx        fcy        fcz
> >
> >    1    1       1000       1000       1000
> >
> > #endif
> >
> >
> >
> > ; Include topology for ions
> >
> > #include "gromos43a1.ff/ions.itp"
> >
> >
> >
> > [ system ]
> >
> > ; Name
> >
> > Protein in water
> >
> >
> >
> > [ molecules ]
> >
> > ; Compound        #mols
> >
> > Protein_chain_A     1
> >
> > PDB               250*6
> >
> > SOL              7217
> >
> > But when I am giving this command “grompp_d -f ions.mdp -c 1r50_solv.gro
> -p
> > topol.top -o ions.tpr” I am getting the following error
> >
> > Fatal error:
> >
> > number of coordinates in coordinate file (solvated.gro, 24888) does not
> > match topology (topol.top, 26388).
> >
> > How will I solve the problem? Please help me out. Here I am attaching the
> > benzene .gro and .itp file.
> >
> > --
> > Swagata Patra
> > M.Tech (Biotech)
> > JRF
> > IIT Guwahati
> >
> > --
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-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati