[gmx-users] Trouble with packing lipids around a protein using InflateGRO

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 8 01:50:18 CEST 2012

On 6/7/12 7:48 PM, Erica Hicks wrote:
> Hi,
> I am working through the KALP-15 in DPPC tutorial (only using a different
> protein) and having difficulties in packing the lipids around the protein.
> After I scaled the lipid positions by a factor of 4 (perl inflategro.pl
> system.gro 4 DPPC 14 system_inflated.gro 5 area.dat) and ran energy
> minimizations (mdrun -v -deffnm em) I tried to scale down the lipids by a
> factor 0.95. However, I did not get the result of the minimization
> (confout.gro). I then received this error:
> Eeeeek! No confout.gro at all!
> Died at inflategro.pl line 81.
> When researching this, I found this comment about the same issue I am having
> troubles with, "that could not have been the command you entered, because
> inflategro.pl is looking for confout.gro, which you have not specified in
> the command." Any suggestions?

If you ran "mdrun -v -deffnm em" then your coordinate file is not named 
confout.gro, it is name em.gro.



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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