[gmx-users] Number of coordinate in topol.top and solv.gro not matching

Sangita Kachhap sangita at imtech.res.in
Wed May 2 14:14:12 CEST 2012

Hello all

I have to do MD simulation of ligand bound membrane protein in lipid bilayer.
Thus I am doing tutorialfor Protein - Ligand tutorial:


I have used following command:

pdb2gmx -f 3HTB_clean.pdb -o conf.gro -water spc

editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0

genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro

grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

I am getting stuck at last command. Its showing following error:

Fatal error:
number of coordinates in coordinate file (solv.gro, 33049)
             does not match topology (topol.top, 33064)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

{But when I calculate number of atom in topol.top and solv.gro it is same}

When I checked above http: I got that such type of error may be due to cpp
variable is not properly set in the .mdp file.
But When I locate ccp in my system and add it to .mdp file.

title           = Minimization  ; Title of run
cpp             =/usr/bin/cpp
; Parameters describing what to do, when to stop and what to save

Then also it showing same error.

Please help me to solve this problem.

I am using gromacs-4.5.5 and installed with fftw-3.3.1 .

With regards
Sangita Kachhap

सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
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