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

Erica Hicks erica.hicks at my.und.edu
Fri Jun 8 01:48:51 CEST 2012


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? 


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