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

[SAPNA BORAH]

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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