AMBER Archive (2004)

Subject: AMBER: MM_PBSA reproduction of literature values and accuracy

From: Karl N. Kirschner (kkirschn_at_hamilton.edu)
Date: Mon Oct 25 2004 - 12:41:34 CDT

Hi all,
  In an attempt to test my understanding of the mm_pbsa procedure I am
trying to reproduce literature values for the solvation free energies of
ethanol. An article (J. Phys. Chem. B 102 (1998) 9571) uses AMBER with
the Cornell et al. force field and HF/6-31G* resp charges, scaled atomic
radii, and a calibrated screening parameter to find a solvation free
energy of -3.46 kcal/mol. This is in reasonable agreement with the
cited experimental value of -4.90 kcal/mol.

  I have attempted to reproduce these results using AMBER8 MM_PBSA,
using the parm94 force field, the same ethanol published charge set
published, and by running a 1 ns simulation of ethanol in explicit TIP3P
waters. Below is the results that I found:

# MEAN STD
# =======================
ELE -13.73 0.32
VDW 0.32 0.23
INT 4.57 1.55
GAS -8.84 1.58
GBSUR 1.42 0.01
GB -7.33 0.25
GBSOL -5.92 0.24
GBELE -21.07 0.28
GBTOT -14.76 1.58
TSTRA 11.21 0.00
TSROT 6.69 0.00
TSVIB 1.53 0.00
TSTOT 19.43 0.00

So, my question comes to is this - have I incorrectly calculated
ethanol's free energy of solvation by incorrectly setting up the mm_pbsa
calculation up? I have even varied the charge set and have not found a
difference in the results to the magnitude I need. I have also viewed
the trajectory using vmd and it appears fine. Below is my input for the
mm_pbsa:

##################
@GENERAL
#
PREFIX ethanol_water_md
PATH ./GenerateSnapshots
#
COMPLEX 0
RECEPTOR 1
LIGAND 0
#
COMPT XXX
RECPT ../ethanol.top
LIGPT XXX
#
GC 1
AS 0
DC 0
#
MM 1
GB 1
PB 0
MS 1
#
NM 1
#
##########
@MAKECRD
BOX YES
NTOTAL 1377
NSTART 50
NSTOP 1000
NFREQ 1
#
NUMBER_LIG_GROUPS 0
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 9
#
################
@TRAJECTORY
TRAJECTORY ../ethanol_water_md.crd
################
@MM
DIELC 1.0
################
@GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
###############
@MS
PROBE 0.0
###############
@NM
DIELC 4
MAXCYC 10000
DRMS 0.01
###############

Any help in my understanding where I might be going wrong, and any
comments the general sense of the accuracy of mm_pbsa would be
appreciated.

Cheers,
Karl 

-- 
---------------------------------
Karl Nicholas Kirschner, Ph.D.
Assistant Professor of Chemistry
Hamilton College, NY 13223
---------------------------------

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