On 10/12/12 2:50 PM, tarak karmakar wrote:
Thanks Justin & Chaban.
Even I did the simulation for 3 ns and it worked well.
Now the issue in my case is , while I was not imposing the M-N
constraints, the metal was rattling around (little bit) and the
histidine residues were moving back and forth (elongation of M-Nhis
length). So I employed constraints to keep them in peace. But I'm bit
worried about the dynamics of the entire protein. I'm not sure how
accurate results these will produce if I impose these sorts of
approximations. Any idea ? Any reference where people have followed
the same ?
Anything you do is going to suffer from the fact that it's an approximation
since MM force fields are not going to preserve coordination geometry for these
ions. A constraint is very rigid, but on average, probably describes correct
behavior. A harmonic interaction is defined by the force constant, but you'll
have a hard time defining proper parameters for that, too. A distance restraint
suffers from a similar interaction regarding how "hard" the interaction is.
Surely a few minutes searching will turn up pertinent literature.
-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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