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

Justin A. Lemkul jalemkul at vt.edu
Wed May 2 15:12:13 CEST 2012

On 5/2/12 8:14 AM, Sangita Kachhap wrote:
> Hello all
> I have to do MD simulation of ligand bound membrane protein in lipid bilayer.
> Thus I am doing tutorialfor Protein - Ligand tutorial:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
> 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

Did you follow the link?  Did you read 

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

That's not possible.

> 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 .

The cpp parameter is ignored for all Gromacs versions as of 4.5.

Your problem is that you don't have a ligand in your coordinate file.  Note that 
you're off by 15 atoms, which is exactly how many are in the ligand described in 
the tutorial.  Go back and read the instructions closely, as appending the 
ligand to the protein coordinate file is discussed in detail.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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