[gmx-users] Re: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology

Justin Lemkul jalemkul at vt.edu
Fri Aug 10 12:15:26 CEST 2012

On 8/10/12 12:57 AM, Bhavaniprasad.V wrote:
> hello justin,
> I got one more error, please help me out again.
> I got the em.gro instead of confout.gro. I reached an area per lipid of ~52 Å2
> for POPE bi layer.
> Next i tried to  add ions to the system after solvating with water. i get the
> following error.
> Program grompp, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/grompp.c, line: 523
> Fatal error:
> number of coordinates in coordinate file (PRO_POPE_sol.gro, 34105)
>               does not match topology (topol.top, 19707)
> Is this difference in the number of atoms due to error in solvating.
> I haven't got this error before.please suggest me what went wrong.

InflateGRO removes all solvent molecules, so this very well could be the source 
of the problem.  Inspect your coordinate file's contents to see where the 
mismatch occurs with respect to the topology.  The solution to this error is 
always a matter of bookkeeping.



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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