Dear Amber users!
Performing several mmgbsa calculations (with NMA for enthropy calculations)
for my test systems I've noticed significant error corrections in the dG
found in final result. From the below log you can find that the order of
such corrections in both cases are equal to the calculated values. Here I
used 100 ns trajectory of the production run of the membrane protein system
as the input for mmgbsa; totally using 50 snapshots both for the entalpy
(each snapshot has been taken every 250000 steps) as well as for the
entropy calculations.
1) Does the enthropy term make main contribution to the errors?
2) Is it possible to reduce its value (e.g using longest MD
trajectories,choosing smaller sampling intervals or do better minimization
as well as method for hessian diagonalization in case of NMA)?
-------------------------------------------------------------------------------
For system1
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Using Normal Mode Entropy Approximation: DELTA G binding = -8.1087 +/-
5.8570
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
For system 2
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Using Normal Mode Entropy Approximation: DELTA G binding = -10.3566 +/-
7.7316
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Thanks for suggestions,
James
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Received on Tue Dec 02 2014 - 13:30:02 PST
