Dear Jason and amber fans,
This is the input file that I used:
==========================================================================================
#
# Input parameters for mm_pbsa.pl
#
# 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 - parmtop file for the complex (not necessary for option GC).
# RECPT - parmtop file for the receptor (not necessary for option GC).
# LIGPT - 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 into individual contributions
# (only works with MM and GB).
#
# MM - Calculation of gas phase 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 md11to35
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./xxx.prmtop
RECPT ./xyz.prmtop
LIGPT ./yyy.prmtop
#
GC 0
AS 0
DC 1
#
MM 1
GB 1
PB 0
MS 0
#
NM 0
#
################################################################################
.DECOMP
DCTYPE 2
COMREC 1-609
COMLIG 610-610
COMPRI 1-610
RECRES 1-609
RECPRI 1-609
RECMAP 1-609
LIGRES 1-1
LIGPRI 1-1
LIGMAP 610-610
################################################################################
.PB
#
# PB parameters (this section is only relevant if PB = 1 above)
#
# The following parameters are passed to the PB solver.
# Additional parameters (e.g. SALT) may be added here.
# For further details see the delphi and pbsa documentation.
#
# PROC - Determines which method is used for solving the PB equation:
# If PROC = 1, the delphi program is applied. If PROC = 2,
# the pbsa program of the AMBER suite is used.
# REFE - Determines which reference state is taken for PB calc:
# If REFE = 0, reaction field energy is calculated with EXDI/INDI.
# Here, INDI must agree with DIELC from MM part.
# If REFE > 0 && INDI > 1.0, the difference of total energies for
# combinations EXDI,INDI and 1.0,INDI is calculated.
# The electrostatic contribution is NOT taken from sander here.
# INDI - Dielectric constant for the molecule.
# EXDI - Dielectric constant for the surrounding solvent.
# SCALE - Lattice spacing in no. of grids per Angstrom.
# LINIT - No. of iterations with linear PB equation.
# PRBRAD - Solvent probe radius in A (e.g. use 1.4 with the PARSE parameter set
# and 1.6 with the radii optimized by R. Luo)
#
# Parameters for pbsa only
#
# RADIOPT - Option to set up atomic avity radii for molecular surface calculation
# and dielectric assignment. A value of 0 uses the cavity radii from the prmtop file.
# A value of 1 sets up optimized cavity radii at the pbsa initialization phase.
# The latter radii are optimized for model compounds of proteins only; use cautions
# when applying these radii to nucleic acids.
#
# Parameters for delphi only
#
# 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 thus equals the value of FOCUS.
# PERFIL - Percentage of the lattice that the largest linear dimension of the
# molecule will fill.
# 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.
#
#
#PROC 2
#3REFE 0
#INDI 1.0
#EXDI 80.0
#SCALE 2.0
#LINIT 500
#PRBRAD 1.6
#
#RADIOPT 1
#
#FOCUS 0
#PERFIL 80.0
#CHARGE ./my_amber94_delphi.crg
#SIZE ./my_parse_delphi.siz
#
#SURFTEN 0.005
#SURFOFF 0.0
#
################################################################################
.MM
#
# MM parameters (this section is only relevant if MM = 1 above)
#
# The following parameters are passed to sander.
# For further details see the sander documentation.
#
# DIELC - Dielectricity constant for electrostatic interactions.
# Note: This is not related to GB calculations.
#
DIELC 1.0
#
################################################################################
.GB
#
# GB parameters (this section is only relevant if GB = 1 above)
#
# 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, 5).
# GBSA - Switches between LCPO (1) and ICOSA (2) method for SASA calc.
# Decomposition only works with ICOSA.
# SALTCON - Concentration (in M) of 1-1 mobile counterions in solution.
# EXTDIEL - Dielectricity constant for the solvent.
# INTDIEL - Dielectricity constant for the solute
#
# SURFTEN / SURFOFF - Values used to compute the nonpolar contribution Gnp to
# the desolvation according to Gnp = SURFTEN * SASA + SURFOFF.
#
IGB 2
GBSA 2
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
.MS
#
# Molsurf parameters (this section is only relevant if MS = 1 above)
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# Since Bondi radii are already augmented by 1.4A, PROBE should be 0.0
#
PROBE 0.0
#
#################################################################################
#.NM
#DIELC 4
#MAXCYC 1000
#DRMS 0.1
#################################################################################
.PROGRAMS
#
# Program executables
#
# DELPHI /home/gohlke/src/delphi.98/exe/delphi
#
################################################################################
=============================================================================================
Then, I got the results as it is now:
I got a lot of energies, I just take TGBTOT as an example. I found every residues got a deltaTGBTOT, including ligand 610. I wonder if the delta TGBTOT for ligand 610 is the binding energy of of 610 with the receptor.
I also tried to compare this values with that obtained by the following input, but I found huge differences between them. Is it expected? If I am only interested in relative binding energy, not absolute one. do you think these two binding energies should follow the same relative order?
=======================================================================================
#
# Input parameters for mm_pbsa.pl
#
# 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 - parmtop file for the complex (not necessary for option GC).
# RECPT - parmtop file for the receptor (not necessary for option GC).
# LIGPT - 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 into individual contributions
# (only works with MM and GB).
#
# MM - Calculation of gas phase 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 md35
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../../prmtop/cpt_wild_complex3.prmtop
RECPT ../../prmtop/cpt_wild_receptor3.prmtop
LIGPT ../../prmtop/cpt_ligand.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 0
MS 0
#
NM 0
#
################################################################################
.PB
#
# PB parameters (this section is only relevant if PB = 1 above)
#
# The following parameters are passed to the PB solver.
# Additional parameters (e.g. SALT) may be added here.
# For further details see the delphi and pbsa documentation.
#
# PROC - Determines which method is used for solving the PB equation:
# If PROC = 1, the delphi program is applied. If PROC = 2,
# the pbsa program of the AMBER suite is used.
# REFE - Determines which reference state is taken for PB calc:
# If REFE = 0, reaction field energy is calculated with EXDI/INDI.
# Here, INDI must agree with DIELC from MM part.
# If REFE > 0 && INDI > 1.0, the difference of total energies for
# combinations EXDI,INDI and 1.0,INDI is calculated.
# The electrostatic contribution is NOT taken from sander here.
# INDI - Dielectric constant for the molecule.
# EXDI - Dielectric constant for the surrounding solvent.
# SCALE - Lattice spacing in no. of grids per Angstrom.
# LINIT - No. of iterations with linear PB equation.
# PRBRAD - Solvent probe radius in A (e.g. use 1.4 with the PARSE parameter set
# and 1.6 with the radii optimized by R. Luo)
#
# Parameters for pbsa only
#
# RADIOPT - Option to set up atomic avity radii for molecular surface calculation
# and dielectric assignment. A value of 0 uses the cavity radii from the prmtop file.
# A value of 1 sets up optimized cavity radii at the pbsa initialization phase.
# The latter radii are optimized for model compounds of proteins only; use cautions
# when applying these radii to nucleic acids.
#
# Parameters for delphi only
#
# 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 thus equals the value of FOCUS.
# PERFIL - Percentage of the lattice that the largest linear dimension of the
# molecule will fill.
# 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.
#
#
#PROC 2
#3REFE 0
#INDI 1.0
#EXDI 80.0
#SCALE 2.0
#LINIT 500
#PRBRAD 1.6
#
#RADIOPT 1
#
#FOCUS 0
#PERFIL 80.0
#CHARGE ./my_amber94_delphi.crg
#SIZE ./my_parse_delphi.siz
#
#SURFTEN 0.005
#SURFOFF 0.0
#
################################################################################
.MM
#
# MM parameters (this section is only relevant if MM = 1 above)
#
# The following parameters are passed to sander.
# For further details see the sander documentation.
#
# DIELC - Dielectricity constant for electrostatic interactions.
# Note: This is not related to GB calculations.
#
DIELC 1.0
#
################################################################################
.GB
#
# GB parameters (this section is only relevant if GB = 1 above)
#
# 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, 5).
# GBSA - Switches between LCPO (1) and ICOSA (2) method for SASA calc.
# Decomposition only works with ICOSA.
# SALTCON - Concentration (in M) of 1-1 mobile counterions in solution.
# EXTDIEL - Dielectricity constant for the solvent.
# INTDIEL - Dielectricity constant for the solute
#
# SURFTEN / SURFOFF - Values used to compute the nonpolar contribution Gnp to
# the desolvation according to Gnp = SURFTEN * SASA + SURFOFF.
#
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
.MS
#
# Molsurf parameters (this section is only relevant if MS = 1 above)
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# Since Bondi radii are already augmented by 1.4A, PROBE should be 0.0
#
PROBE 0.0
#
#################################################################################
#.NM
#DIELC 4
#MAXCYC 1000
#DRMS 0.1
#################################################################################
.PROGRAMS
#
# Program executables
#
# DELPHI /home/gohlke/src/delphi.98/exe/delphi
#
################################################################################
=============================================================================================
Many thanks in advanced.
Best regards,
_________________________________________________________________
Hotmail: Trusted email with powerful SPAM protection.
https://signup.live.com/signup.aspx?id=60969
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 31 2010 - 21:00:04 PDT
