Dear AMBER users,
I have some common doubt about the MMGB/PBSA decomposition methods.
[1] Wen I did the free energy decomposition for pairs resid 1 and
resid 2 similar values but slightly different values. for example: 1
and 2 the total value is -6.173 and for 2 and 1 the value is -6.154.
The small difference comes from the term non-polar solvation. All
other values are exactly the same.
[2] The previous peril scrpit will divide the total decomposition
between the pair. Is that the same procedue follow here in MMPBSA.py?
For example if we do the QM calculation on the residues 1 and 2, the
calculated interaction energy is ~13 kcal mol-1. So i assume that the
binding free energy splitted between the two residues..So in order to
comapre with the QM values we have to double it. If I am wrong pls
correct me..
[3] How the solvation free energy terms decompose. ? Since solvation
free energy does not do anything with the other residues, Wat is the
significance of this decomposition terms?
[4] Is there any way to performe intra strand decomposition? I have
performed decomposition between two modified DNA chains each
containing 10 residues. When I did decompostion for all the 20
residues, the decomposition energy values for the 1-2, 1-3, 1-4
...1-9, 1-10 are 0.000 for all terms..I thought it would print the
intrastrad binding free energy terms too..
[5] The polar solvation decomposition value for the 2-2, 3-3, 4-4
(dont know wat is the significance of the interaction of the residue
with itself) prints some + values like +4 kcal mol-1..Wat does it
mean?
I hope these questions can help others too as I could nt find any
details from manual....
Thanks
Rajesh
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Received on Mon Sep 26 2011 - 12:30:06 PDT
