On 3/28/13 4:24 PM, Алексей Раевский wrote:
Hi dear All!
Good day dear forum! I have a question abour freezing of atoms during MD.
The idea is that - I have a protein and one domain contains a site. Also I
have two ligands, one of them is better inhibitor in comparison with
another one. To prepare the topology of the inhibitor I need to use a
R.E.D.III server. As there are several different fitting methods, so I have
to carry out a series of short MDs (about 5-10 ns) for each of them. The
question is - is it possible to isolate this domain and fix/freeze last
residues of the hairpin/linker to prevent movement of domain segments? I
know that this is not the way to study ligand-protein interaction, however
I just want to use it for understanding which topology generation method is
better.
You can freeze whatever group you want using freezegrps and a custom index
group. It is also reasonably simple to restrain a segment of the structure
using normal position restraints (again, created with a custom index group).
-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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