dear users,
i am trying md simulation for dna+protein system ...but i don't want
to take combined crystallographic structure from pdb bank.
My problem is that if i take separate structure of protein and and
separate DNA structure from pdb bank and merge it in common pdb file
...then how i will ensure that after minimization and long md run,
protein will go and attach to DNA with lowest free energy ...because
it can get trap to any random position with not the lowest possible
structure.
Moreover, placing protein close to DNA and then after MD checking free
energy is not feasible , as i need to search for as many orientation
of protein near DNA for best feasible protein-DNA structure.
I was thinking of doing it with ROSETTA , but is there any better
option in AMBER or any software.
yours suggestions will be valuable to me.
-- Regards
NAJMUL ARFIN
Research Scholar
SCHOOL OF PHYSICAL SCIENCES,
JAWAHARLAL NEHRU UNIVERSITY,
NEW DELHI -110067
+919910040525
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Received on Wed Aug 22 2012 - 12:00:04 PDT
