Hello all
I have a modelled protein - DNA complex in protein C-terminus has 16 residues
radom coil.
It is hypothesized that this region folds into a alpha helix when bound to
DNA.So here I
want to use REMD.It has total 2688 atoms as first step is to determine number of
replicas.
As according to amber tutorial :-
http://ambermd.org/tutorials/advanced/tutorial7/
number of replica is determine according to square root of number of total
atoms, as my
sytem have total 2688 atoms and its square root is ~51 so should I consider
number of replica
51?
So kindly suggest me.
With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Sat Dec 25 2010 - 05:00:02 PST
