[gmx-users] Re: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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