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

Swagata Patra swagataliza at gmail.com
Mon Feb 8 15:06:02 CET 2016

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, which are:

1‐ Determine the number of co‐solvent molecules necessary, given the box
dimensions of your system.

2‐ Generate a coordinate file of a single molecule of your co‐solvent
(i.e., urea.gro).

3‐ Use the ‐ci ‐nmol options of genbox to add the required number of co‐solvent
molecules to the box.

4‐ Fill the remainder of the box with water (or whatever your other solvent
is) using genbox.

5‐ Edit your topology to #include the appropriate .itp files, as well as
make changes to the [ molecules ] directive to account for all the species
in your system.

 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

> 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"


; Include benzene topology

#include "benz.itp"

; Include water topology

#include "gromos43a1.ff/spce.itp"


; Position restraint for each water oxygen

[ position_restraints ]

;  i funct       fcx        fcy        fcz

   1    1       1000       1000       1000


; 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)
IIT Guwahati

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