Hi,
I run the 02_MMPBSA_Stability tutorial of MM_PBSA in the amber7
distribution,
using Delphi 4.1
I found, on average, that the corrected reaction field energy is 10Kt
lower
than what reported in the ras_raf_II_wt_statistics.out.save file.
Did anybody else noticed a difference? Has the tutorial been run with a
different
version of Delphi?...
The input file:
#
# Input parameters for mm_pbsa.pl
# This example uses snapshots from ../01_GenerateSnapshots, and computes
# continuum free energy estimates, using both GB and PB models
#
# Holger Gohlke
# 08.01.2002
#
################################################################################
.GENERAL
#
# General parameters
# 0: means NO; >0: means YES
#
# mm_pbsa allows to calculate (absolute) free energies for one
molecular
# species or a free energy difference according to Receptor + Ligand
= Complex,
# DeltaG = G(Complex) - G(Receptor) - G(Ligand).
#
# PREFIX - To the prefix, "{_com, _rec, _lig}.crd.Number" is added
during
# generation of snapshots as well as during mm_pbsa
calculations.
# PATH - Specifies the location where to store or get snapshots.
# COMPLEX - Set to 1 if free energy difference is calculated.
# RECEPTOR - Set to 1 if either (absolute) free energy or free energy
difference
# are calculated.
# LIGAND - Set to 1 if free energy difference is calculated.
#
# COMPT - Name of the parmtop file for the complex (not necessary for
option GC).
# RECPT - Name of the parmtop file for the receptor (not necessary for
option GC).
# LIGPT - Name of the parmtop file for the ligand (not necessary for
option GC).
#
# GC - Snapshots are generated from trajectories (see below).
# AS - Residues are mutated during generation of snapshots from
trajectories.
# DC - Decompose the free energies in single contributions (only works
with MM and GB yet).
#
# MM - Calculation of gasphase energies using sander.
# GB - Calculation of desolvation free energies using the GB models in
sander (see below).
# PB - Calculation of desolvation free energies using delphi (see
below).
# MS - Calculation of nonpolar contributions to desolvation using
molsurf (see below).
# If MS == 0, nonpolar contributions are calculated with the LCPO
method in sander.
# NM - Calculation of entropies with nmode.
#
PREFIX ras_raf_II_wt
PATH ../01_GenerateSnapshots/
COMPLEX 1
RECEPTOR 0
LIGAND 0
#
COMPT ../ras_raf_II_wt.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 1
MS 1
#
NM 0
#
################################################################################
.DELPHI
#
# Delphi parameters
#
# The first group of the following parameters are passed to delphi.
# Additional parameters (e.g. SALT) may be added here.
# For further details see the delphi documentation.
#
# FOCUS - If FOCUS > 0, subsequent (multiple) PERFIL and SCALE
parameters are
# used for multiple delphi calculations using the focussing
technique.
# The # of _focussing_ delphi calculations thereby equals the value
of FOCUS.
# INDI - Dielectricity constant for the molecule.
# EXDI - Dielectricity constant for the surrounding solvent.
# PERFIL - Percentage of the lattice that the largest linear dimension
of the
# molecule will fill.
# SCALE - Lattice spacing in no. of grids per Angstrom.
# LINIT - No. of iterations with linear PB equation.
# BNDCON - Type of boundary condition.
# CHARGE - Name of the charge file.
# SIZE - Name of the size (radii) file.
#
# SURFTEN / SURFOFF - Values used to compute the nonpolar contribution
Gnp to the
# desolvation according to Gnp = SURFTEN * SASA +
SURFOFF.
#
FOCUS 0
INDI 1.0
EXDI 80.0
PERFIL 80.0
SCALE 2
LINIT 1000
BNDCON 4
CHARGE ../my_amber94_delphi.crg
SIZE ../my_parse_delphi.siz
#
SURFTEN 0.00542
SURFOFF 0.92
#
################################################################################
.GB
#
# GB parameters
#
# The first group of the following parameters are passed to sander.
# For further details see the sander documentation.
#
# IGB - Switches between Tsui's GB (1), Onufriev's GB (2),
# Jayaram's et al. GB (3) or Jayaram's et al. MGB (4).
# SALTCON - Concentration (in M) of 1-1 mobile counterions in
solution.
# EXTDIEL - Dielectricity constant for the surrounding solvent.
#
# SURFTEN / SURFOFF - Values used to compute the nonpolar contribution
Gnp to the
# desolvation according to Gnp = SURFTEN * SASA +
SURFOFF.
#
IGB 4
SALTCON 0.00
EXTDIEL 80.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
.MS
#
# Molsurf parameters
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# RADII - Name of the radii file.
#
PROBE 1.4
RADII ../atmtypenumbers
#
#################################################################################
.PROGRAMS
#
# Program executables
#
DELPHI /usr/local/SW/delphi/release1_1/exe/delphi
#
################################################################################
My output file:
MM
GB
PB
MS
1
BOND = 693.4575 ANGLE = 1895.7111 DIHED =
1478.8198
VDWAALS = -1974.0288 EEL = -17194.5212 EGB =
-2773.2755
1-4 VDW = 866.5634 1-4 EEL = 7173.9328 RESTRAINT =
0.0000
corrected reaction field energy: 0.0000 kt
corrected reaction field energy: -6907.466 kt
surface area = 11380.021
2
BOND = 702.5472 ANGLE = 1864.7257 DIHED =
1470.3932
VDWAALS = -1971.3785 EEL = -17225.7579 EGB =
-2790.6269
1-4 VDW = 858.8716 1-4 EEL = 7254.3905 RESTRAINT =
0.0000
corrected reaction field energy: 0.0000 kt
corrected reaction field energy: -6975.049 kt
surface area = 11418.709
3
BOND = 709.2830 ANGLE = 1868.8221 DIHED =
1458.3179
VDWAALS = -1978.0629 EEL = -17204.9664 EGB =
-2787.5404
1-4 VDW = 866.4882 1-4 EEL = 7199.6052 RESTRAINT =
0.0000
corrected reaction field energy: 0.0000 kt
corrected reaction field energy: -6988.980 kt
surface area = 11427.770
4
BOND = 734.7567 ANGLE = 1903.6052 DIHED =
1444.6601
VDWAALS = -1957.8047 EEL = -17204.4384 EGB =
-2797.1264
1-4 VDW = 861.9518 1-4 EEL = 7170.7310 RESTRAINT =
0.0000
corrected reaction field energy: 0.0000 kt
corrected reaction field energy: -6904.362 kt
surface area = 11309.241
5
BOND = 755.6136 ANGLE = 1850.9879 DIHED =
1480.1951
VDWAALS = -1978.4081 EEL = -17145.3442 EGB =
-2823.9887
1-4 VDW = 860.5483 1-4 EEL = 7187.4484 RESTRAINT =
0.0000
corrected reaction field energy: 0.0000 kt
corrected reaction field energy: -7008.397 kt
surface area = 11452.367
My statistics file:
# MEAN STD
# =======================
ELE -9997.78 32.24
VDW -1109.05 8.26
INT 4062.38 24.18
GAS -7044.46 34.03
PBSUR 61.87 0.30
PBCAL -4147.17 28.61
PBSOL -4085.31 28.34
PBELE -14144.96 16.63
PBTOT -11129.76 34.74
GBSUR 82.06 0.40
GB -2794.51 18.64
GBSOL -2712.45 18.51
GBELE -12792.30 25.07
GBTOT -9756.91 19.97
--
Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Universita di Modena e Reggio Emilia
Via Campi 183
41100 Modena - ITALY
-------------------------------------
tel 0039-059-2055145
fax 0039-059-2055131
-------------------------------------
Received on Thu Oct 10 2002 - 07:22:59 PDT
