On 1/9/13 6:02 AM, Алексей Раевский wrote:
Hi this is a repost, maybe it was missed.
I want to create a system with hybrid solvent (explicit/implicit). My
system is large enough to calculate it with explicit SOL. But it is
critical to study the behavior of several water molecules in the site. The
idea is to generate a layer of explicit water molecules around the protein
molecule with ligand in the binding site and than fill the box with
continuous imlicit solvent with epsilon = 80. To prevent the departure of
discrete water molecules into the implicit layer I want to limit the
distance of their movement with something like PULL COM distance or
anything else. Is it real or I have to find another way or choose another
software for this purpose.
Perhaps something like a spherical restraint would be more useful than the pull
code, as was done in http://www.pnas.org/content/108/17/6838. The spherical
restraint potential has been implemented in the master development branch, and
thus won't appear in the next release (4.6) but perhaps you can easily patch the
source to use this feature. I have no idea how that will play with an external
implicit environment, but it's probably worth a shot.
-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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