Dear Amber Users,
I am trying to obtain pairwise interaction energies between amino acid residues
from mm_pbsa. The interaction energies obtained (Eele+Evdw+Eint) are the gas
phase energies as suggested in the tutorial. However, a more realistic value
would be the interaction energy taking into consideration the solvent effect.
So Eint = Egas+Esolvent
= Eij + Ei-solv + Ej-solv
where i, j are two residues and solv is the solvent.
>From the parameters obtained from the decomposed pairwise interaction energies,
is it possible to derive the above.
Or is it that I am going wrong somewhere in the basic understanding.
I would be grateful if someone please clarifies my confusion.
Thanks a lot in advance.
Sincere Regards,
Moitrayee
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Received on Mon Aug 23 2010 - 03:30:03 PDT
