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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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