[gmx-users] Error in system_inflate.gro coordinates does not match

Justin Lemkul jalemkul at vt.edu
Wed Jul 9 13:47:45 CEST 2014

On 7/9/14, 6:17 AM, RINU KHATTRI wrote:
> hello every one
> I am working on complex with popc membrane i did
> perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
> after this step minimization
> grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
> i got error
> Fatal error:
> number of coordinates in coordinate file (system_inflated.gro, 10224)
>               does not match topology (topol.top, 10245)
> i have been removed 6 lipid molecules in my topology file according to
> output i got one thing new in my system_inflate.gro file the written
> displayed atom is 10224 but after counting it is 10536 so if i correct it
> difference is more

I don't know what this means, but the number of atoms that grompp is finding is 
going to be correct.

> in topology file [molecule]
> protein chain 1
> UNK            1
> POPC 122
> how to resolve  it

I would venture a guess that UNK has 21 atoms.  I don't know that InflateGRO 
handles arbitrary molecules, so it may have gotten deleted upon inflation. 
Check system_inflated.gro; it will be very obvious if it is missing.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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