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

Justin Lemkul jalemkul at vt.edu
Fri Jul 11 23:24:15 CEST 2014

On 7/11/14, 3:18 AM, RINU KHATTRI wrote:
> hello
> i am following the lysozyme tutorial
> editconf -f system_shrink20.gro -o newbox.gro -bt dodecahedron -d 1.0

Don't alter the box like this; it's totally nonsensical.

>   solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
>   but after running second command i got error  solvate command not found
> gmx solvate is also not working

The tutorial corresponds to version 5.0; if you're using an older version, the 
command is called "genbox."



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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