Hi,
I am doing mm_pbsa on high charged system as RNA with Amber8.0. While
some ligand also has negative charge (toward solvent) the PBTOT and
GBTOT will be positive as below. And the ligand with different
charges will give much more difference in PB and GB. It's hard to
compare different ligand's energy.
How to deal with such situation. I use the default parameters in
mm_pbsa.
Thank you
suxin
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE 4009.76 0.00
VDW -24.66 0.00
INT 0.12 0.00
GAS 3985.23 0.00
PBSUR -2.55 0.00
PBCAL -3914.80 0.00
PBSOL -3917.35 0.00
PBELE 94.96 0.00
PBTOT 67.88 0.00
GBSUR -3.67 0.00
GB -3941.00 0.00
GBSOL -3944.67 0.00
GBELE 68.76 0.00
GBTOT 40.56 0.00
-----------------------------------------------------------------
Suxin Zheng
Research Associate, Varani Group
Box 351700
Department of Chemistry, University of Washington
Seattle, WA, 98195-1700
sxzheng.u.washington.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Aug 20 2006 - 06:07:06 PDT
