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

Sotirios Dionysios I. Papadatos si.papadatos at edu.cut.ac.cy
Mon Feb 8 15:43:46 CET 2016

Hi, in general the error is self explanatory. It means that you have set more atoms in the topology file (usually that is the case).
I would suggest a simple script in the language that you are most comfortable with, to count the occurrences of a specific element.
Hope this helps.  

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Swagata Patra <swagataliza at gmail.com>
Sent: Monday, February 8, 2016 4:05 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] topology and coordinate file not matching after grompp

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 ¨Cci ¨Cnmol 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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