[gmx-users] (no subject)

Justin Lemkul jalemkul at vt.edu
Sun Nov 9 01:05:00 CET 2014

On 11/8/14 6:53 PM, Thomas Lipscomb wrote:
> Dear gmx-users,
> I am still following this tutorial:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
> But I got an error at this step:
> "Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called "confout.gro"):
> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat"
> [tlipscomb at prime-radiant KALP]$ perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
> Eeeeek! No confout.gro at all!

As the error says, the file "confout.gro" does not exist.  Either (1) you named 
it something else, (2) energy minimization failed for some reason, or (3) it's 
somewhere else on your file system.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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