FEP simulation on membrane protein

From: Kapil jain (noxtreme007_at_gmail.com)
Date: Sun Jul 21 2013 - 22:37:44 CDT


I'm trying to do FEP calculations by point mutation of certain amino acids
on a membrane protein. I have certain questions which I need to clarify
before going ahead.

1. I have mutated the residue in al1b (protein) with mutator pluggin in VMD
and generated both the mutated.psf and .pdb files along with the
mutated.fep and .fep.psf files for FEP calculations. So which file I should
use to proceed ahead with the FEP calculations?

2. If I make use of either of the two .psf and .pdb files generated for
mutated and FEP, Do I have to start form the beginning by melting of lipid
tails followed by minimization and equilibration and then the production

3. How long the production run should be to calculate the free energy

4. In tutorial for FEP calculations, one need to calculate the free energy
in vacuo and other in bulk water, but since it is a membrane protein and
already solvated, how should I calculate the free energy in vacuo as it is
surrounded by lipid tails and water molecules.?



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