[gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093)

Justin Lemkul jalemkul at vt.edu
Wed Feb 27 17:53:53 CET 2013

On 2/27/13 11:14 AM, swati rana wrote:
> Thanx a lot that helped... but now there is one more issue. I am consulting
> the site for each and every error and getting most of the help but these
> are few which i am not able to resolve even after referring to the site.
> After running the energy minimization step i am facing the following error:
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/confio.c, line: 801
> Fatal error:
> Something is wrong in the coordinate formatting of file system.gro. Note
> that gro is fixed format (see the manual)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> I am not able to understand that in system.gro file do we have to do the
> change in the no of atoms according to the inflated_system.gro file or not.

No, the number of atoms in the coordinate file should be correct.  InflateGRO 
does this for you.

> Another thing is if i am adding Chloride ions to equalize the charge do i
> have to reduce the no of POPC molecules or not. Kindly suggest what should

During inflation and shrinking, you should not be adding solvent or ions.  You 
will get a nonsensical result.

> be done i looked into the system.gro file and also the line it is referring
> to i did not find anything unusual. But there is a catch its the same
> molecule LEU which was having link to NH3.

Probably a visualization artifact.  Real bonds are set in the topology, not in 
whatever the visualization program guesses.



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


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