On 4/2/13 6:07 AM, alex rayevsky wrote:
Dear All!
I have a doubt about the rightness of ligand/molecule integration in the
topology file. I'm using an amber (tleap) or swissparam.ch to build a
topology of the residue (modified trna). Is it neccessary to generate a
position restrain file (genrestr program) for this residue or not? I've
started both dynamics with/without posrestraints on my residue, however I'm
really not sure that my results from both of them are different. But I want
to do everything in right way, so what can you say about this?
Restraints during equilibration are used to prevent unnatural forces from the
unequilibrated solvent and help prevent deformation of the structure. It's
never a bad idea to restrain the whole solute. If I were reading a paper that
described restraining the whole solute, except for one residue because it was
special or difficult to deal with, I would immediately be suspicious.
-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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