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

[Tsjerk Wassenaar]

Hi Swagata,

You can't use expressions: 250*6

Cheers,

Tsjerk
On Feb 9, 2016 06:34, "Swagata Patra" <swagataliza at gmail.com> wrote:

> 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
> > >
> > > --
> > > Gromacs Users mailing list
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>
>
>
> --
> Swagata Patra
> M.Tech (Biotech)
> JRF
> IIT Guwahati
> --
> Gromacs Users mailing list
>
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> posting!
>
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>
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