On 4/19/13 7:37 AM, Giuseppe wrote:
Dear Justin,
thank you very much for replying. When I run the editconf tool I set for
sure the right box vectors (6.23910 6.17970 6.91950) so that in the
system.gro file (according to the nomenclature of your tutorial) the box
vectors from the protein structure and from the membrane are the same, but i
noticed that, after using the perl tool, they magically changed (e.g. in the
system_inflated.gro file they became 24.95640 24.71880 6.91950). Maybe
That's not magic, it's what InflateGRO does. It expands the membrane outward,
thus changing the box vectors.
something is wrong with the "-center" option? I include the complete
editconf command that I run: "editconf -f protein_processed.gro -o
protein_newbox.gro -c -box 6.23910 6.17970 6.91950 -rotate 85 -10 55
-center 8 8 6". Thanks for your patience and your appreciated help.
Here's your problem. First, -c and -center do not play well with one another.
The -c option centers the protein at (vector/2) in each dimension. Then you're
manually specifying a center with -center, so -c is overridden. Moreover, the
values provided to -center make no sense, since they place the protein outside
of the box. Either use -c or a sensible setting for -center, whichever makes
sense in your case.
-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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