On 1/16/13 8:26 PM, Kieu Thu Nguyen wrote:
@Justin, i am trying to simulate oligomerization of membrane protein. I
want to assemble a big box with proteins from many small box having a
protein. Is it available ?
The method I described previously should work. You place one patch (membrane +
embedded protein) at some location within a large box using editconf -center,
then combine with any other system(s) that have similarly been positioned using
editconf -center. The tutorial I linked before demonstrates a trivial example
of something similar, but it illustrates the logic behind the process. You
won't get any clashes to be automatically resolved/molecules deleted, but even
with small gaps or unequilibrated boundaries, a gentle equilibration protocol
should resolve those issues.
-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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