[gmx-users] error coordinates in .gro donnot match .top

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 5 12:35:28 CEST 2009

Asmaa Elsheshiny wrote:
> Hi, all
> when I want to use gromacs preprocessor grompp to obtain  .tpr to use in the energy minimization as follow
>  grompp -f minim.mdp -c bradywaterbox.gro -p brady.top -o minimbrady.tpr
> I got the following error message
> Fatal error:
> number of coordinates in coordinate file (bradywaterbox.gro, 670)
>              does not match topology (brady.top, 0)
> where,  bradywaterbox.gro & brady.top are obtained from 
> genbox -cp solvatedbrady.gro -cs spc216.gro -o bradywaterbox.gro -p brady.top
> I think that the topology file didnot include the solvent molecules so it canont be mached with the coordinate file .gro , did it?
> So how can I fix this problem?

There is a section regarding this error here:


grompp doesn't seem to think your topology has anything in it at all, so it's 
not simply an issue of the waters.


> Regards,
> Asmaa 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


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


More information about the gromacs.org_gmx-users mailing list