Hi Marcin,
Not sure this is answered or not ...
The confusion originates from the different default settings in MMPBSA perl
script and sander for nonpolar solvation free energies.
If you turn on the option of NPOPT = 2, you can get desired output without
setting any more parameters, i.e. the default values inside sander
(CAVITY_SURFTEN = 0.04356 and CAVITY_OFFSET = -1.008) are for NPOPT = 2.
All the best,
Ray
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun May 25 2008 - 06:07:36 PDT
