Sir,
I would like to examine the 'most stable' conformation of the 240aa
protein (HOMOLOGY MODELLED) - it has no PDB coordinates.I want to
minimize it and later run a MD simulation in explicit
solvent(TIP3P)with DIELECTRIC=1, constant pressure.As i am new to AMBER
, have certain doubts 1)what parameters i need to consider for
minimisation then eqilibration then production.
2) At the minimisation level how i can know that protein has reached to
its convergence .
Thanks in advance
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Received on Thu Mar 04 2010 - 03:30:04 PST
