minnale wrote:
Hi all,
I have two doubts on PR, may be these are trivial to you.
1.According to Gromacs procedure(from Gromacs tutorial) the sequential
steps are (a)Energy minimisation (b)Position restrain with force
constant descendant manner and finally (c)production. Here my doubt
that, is it require to do energy minimisation between PR and production?
because after PR the system equilibrating properly if do one
minimisation the structure looses bad contacts with low energy, am I
right?
There is no need to run EM after PR. EM simply gives the system a reasonable
starting point, energetically speaking.
2.If my desire protein contain some missing residues(from PDB)rectified
those residues by using INSIGHT-II. Later start simulations particularly
at PR, is it require to keep restrain specifically on added missing
residues or whole protein residues in .itp file?
I don't see any reason not to restrain the entire protein, as long as it is
intact.
-Justin
Any suggestions would be appreciated
Thanks in advance.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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