AMBER Archive (2007)

Subject: AMBER: nonpolar solvation energy

From: khn _ (khnb3_at_yahoo.com)
Date: Wed Jan 31 2007 - 10:33:55 CST

hi all

i have a question regarding MMPBSA in amber8
since the program doesnt calculate the solute-solvent
vdW interaction or the dispersion contribution as
regard to the nonpolar solvation energy, is there any
way that i could do it manually? my knowledge is quite
limited, can i do it by running sander in explicit
solvent for each extracted snapshot and just take the
vdW contribution? but the values would be so huge, is
that correct? because it would involve solvent-solvent
interaction as well (is it?) and how many steps should
i run? is it enough if just 1 step? i really need
someone to guide me on this

i know that in amber9, the dispersion contribution has
been implemented in PBSA, thats really neat but i dont
have amber9.

if there are other suggestions on how i should extract
the solute-solvent vdW contributions, please shout
out, i would definitely definitely appreciate it very
very much!

thanks all

 
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