AMBER Archive (2004)

Subject: AMBER: question about mmpbsa

From: xhu1_at_memphis.edu
Date: Tue Dec 07 2004 - 19:20:19 CST

Dear Amber Users,

I am using amber 7 to do mmpb(gb)sa calculations.In the sample perl
script, for GB calculation, IGB=4 and MGB is used. MGB assumes an
internal dielectric of 2 (J. of Comput Chem 2004 25:265, Michael Feig,
Alexey Onugeriev...). However, for PB calculation using Delphi,
INDI=1. If I want to compare the PB value with GB value (gotten from
this perl script), I should setup INDI=2, and PBTOT = PBCAL + PBSUR +
1/2 * ELE + VDW + INT(because ELE is for internal/external dielectruc
constant =1). Am I right? The reason I ask is when I set INDI=2, the
script looks like still using ELE, not half ELE to calculate the
PBTOT.

The following are the results of the example mmpbsa binding job in
amber(amber7/src/mm_pbsa/Examples/03_MMPBSA_Binding), with INDI =1 and
2 respectively.

INDI=1(agree with the ras_raf_II_wt_statistics.out.save)
   
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -1287.43 18.06
VDW -61.29 1.40
INT 0.00 0.00
GAS -1348.73 18.01
PBSUR -3.42 0.08
PBCAL 1330.46 12.06
PBSOL 1327.04 12.09
PBELE 43.03 13.72
PBTOT -21.68 14.41
GBSUR -4.42 0.10
GB 1310.48 13.82
GBSOL 1306.06 13.89
GBELE 23.05 5.00
GBTOT -42.67 5.52

INDI=2

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -1287.43 18.06
VDW -61.29 1.40
INT 0.00 0.00
GAS -1348.73 18.01
PBSUR -4.25 0.08
PBCAL 655.37 6.17
PBSOL 651.12 6.20
PBELE -632.06 14.70
PBTOT -697.61 14.97
GBSUR -4.42 0.10
GB 1310.48 13.82
GBSOL 1306.06 13.89
GBELE 23.05 5.00
GBTOT -42.67 5.52

Please feel free to correct me. Thank you so much!

Regards

Shawn Hu

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