Dear Amber users,
I am attempting to calculate the entropic contribution to the binding
energy of a very large system and previously I had thought about truncating
the system and using NMode but eventually decided against it because the
protein has a very obvious correlated motion of its monomers and upon
binding that motion is almost lost so the quasi-harmonic approximation
would probably be pertinent to this case.
The number of atoms being 6000 + I need at least 18 000 frames for the
quasi-harmonic approximation. So I now have three separate trajectories
(one of the protein, one of the complex and one of the ligand -- I wanted
to use separate trajectories precisely because upon binding the motion of
the protein changes), each having 250 000 frames.
I started an MMPBSA calculation using these three trajectories and using
all 250 000 frames and at the rate at which the frames are being processed
right now, I anticipate at least 3-4 days will be spent just on the GB
calculations, and I can't estimate how much the entropy calculation will
take and whether everything will run smoothly or not from now on.
Since obtaining this entropy is a little time-sensitive now, I was thinking
if maybe I could reduce the number of frames needed for the quasi-harmonic
calculation by removing all hydrogen atoms from the trajectory. This would
reduce the number of frames needed by roughly a half. I was thinking about
doing two MMPBSA calculations: one using a trajectory with all of the
hydrogens present, from which I would derive the intramolecular energy and
the solvation energy and one using a trajectory that is free of hydrogens,
from which I would simply derive the entropy. I recall reading about
something similar in an article but am not sure I remember correctly. Is
this a valid procedure?
If not could someone tell me if an MMPBSA calculation can be restarted if
it dies for whatever reason and how? I know there is an option to use the
existing input files, but I am not sure if this means that the script will
pick up where it left off if it died in the middle of frame processing for
example.
Thank you!
Laura
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Received on Sun Apr 26 2015 - 21:00:02 PDT
