AMBER Archive (2008)

Subject: RE: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations

From: moitrayee_at_mbu.iisc.ernet.in
Date: Thu Oct 30 2008 - 00:56:51 CDT

The results are as follows:-

# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -8580.92 75.32 -8373.88 76.58 181.80 6.24
VDW -1302.30 27.49 -1272.66 26.87 7.95 2.28
INT 6559.52 49.74 6450.34 49.59 109.18 6.94
GAS -3323.70 89.69 -3196.19 91.01 298.92 7.54
PBSUR 97.18 0.93 99.37 0.94 6.81 0.04
PBCAL -3261.74 66.78 -3468.90 68.12 -144.89 4.03
PBSOL -3164.56 66.28 -3369.52 67.62 -138.08 4.03
PBELE -11842.66 34.34 -11842.78 35.19 36.91 4.01
PBTOT -6488.26 52.50 -6565.72 51.92 160.85 6.15
GBSUR 97.18 0.93 99.37 0.94 6.81 0.04
GB -3328.93 65.57 -3476.23 66.92 -135.94 4.20
GBSOL -3231.75 65.07 -3376.86 66.42 -129.13 4.19
GBELE -11909.85 29.47 -11850.11 29.51 45.86 3.86
GBTOT -6555.45 51.01 -6573.05 51.22 169.79 6.81

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -388.84 15.45
VDW -37.59 6.95
INT -0.00 0.00
GAS -426.43 13.04
PBSUR -9.01 0.20
PBCAL 352.05 11.42
PBSOL 343.04 11.42
PBELE -36.79 12.43
PBTOT -83.39 9.35
GBSUR -9.01 0.20
GB 283.24 9.92
GBSOL 274.23 9.93
GBELE -105.60 10.56
GBTOT -152.20 7.43

Thanks a lot.

Sincere Regards,
Moitrayee

> It seems that you are using identical charges and radii for both PB and GB.
> It would be easier to spot any problem if we can take a look of your results
> from mmpbsa script.
>
> All the best,
> Ray
>
> ==========================================
> Ray Luo, Ph.D.
> Associate Professor
> Dept Molecular Biology & Biochemistry
> University of California, Irvine, CA 92697
> USPS: PO Box 3900 Email: rluo_at_uci.edu
> Phones: (949) 824-9528, 9562
> Web: http://rayl0.bio.uci.edu/
> ==========================================
>
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> moitrayee_at_mbu.iisc.ernet.in
> Sent: Wednesday, October 29, 2008 6:07 AM
> To: amber_at_scripps.edu
> Subject: AMBER: Huge difference between pbtot and gbtot in mm-pbsa
> calculations
>
> Dear Amber Users,
>
> I am doing a free energy calculation for a complex using mm-pbsa method. My
> output shows a huge difference between PBTOT and GBTOT, GBTOT being almost
> doubly negetive than PBTOT. My input for energy calculation is as follows:
> #
> # 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
> # 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).
> # Calculation of nonpolar solvation free energies according to
> # the NPOPT option in pbsa (see below).
> # MS - Calculation of nonpolar contributions to desolvation using molsurf
> # (see below).
> # If MS == 0 and GB == 1, nonpolar contributions are calculated with
> the
> # LCPO method in sander.
> # If MS == 0 and PB == 1, nonpolar contributions are calculated
> according
> # the NPOPT option in pbsa (see below).
> # NM - Calculation of entropies with nmode.
> #
> PREFIX snapshot
> PATH ../gensnapshots
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ./1xxx_yyy.prmtop
> RECPT ./1xxx.prmtop
> LIGPT ./yyy.prmtop
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 1
> PB 1
> MS 1
> ##
> NM 0
> #
> ############################################################################
> ####
> @PB
> #
> # PB parameters (this section is only relevant if PB = 1 above)
> #
> # The following parameters are passed to the PB solver.
> # Additional input parameters may also be added here. See the sander PB
> # documentation for more options.
> #
> # PROC - Determines which method is used for solving the PB equation:
> # By default, PROC = 2, the pbsa program of the AMBER suite is
> used.
> # REFE - Determines which reference state is taken for PB calc:
> # By default, REFE = 0, reaction field energy is calculated with
> # EXDI/INDI. Here, INDI must agree with DIELC from MM part.
> # INDI - Dielectric constant for the solute.
> # EXDI - Dielectric constant for the surrounding solvent.
> # ISTRNG - Ionic strength (in mM) for the Poisson-Boltzmann solvent.
> # PRBRAD - Solvent probe radius in Angstrom:
> # 1.4: with the radii in the prmtop files. Default.
> # 1.6: with the radii optimized by Tan and Luo (In preparation).
> # See RADIOPT on how to choose a cavity radii set.
> # RADIOPT - Option to set up radii for PB calc:
> # 0: uses the radii from the prmtop file. Default.
> # 1: uses the radii optimized by Tan and Luo (In preparation)
> # with respect to the reaction field energies computed
> # in the TIP3P explicit solvents. Note that optimized radii
> # are based on AMBER atom types (upper case) and charges.
> # Radii from the prmtop files are used if the atom types
> # are defined by antechamber (lower case).
> # SCALE - Lattice spacing in no. of grids per Angstrom.
> # LINIT - No. of iterations with linear PB equation.#
> # NP Parameters for nonpolar solvation energies if MS = 0
> #
> # NPOPT - Option for modeling nonpolar solvation free energy.
> # See sander PB documentation for more information on the
> # implementations by Tan and Luo (In preparation).
> # 1: uses the solvent-accessible-surface area to correlate total
> # nonpolar solvation free energy:
> # Gnp = CAVITY_SURFTEN * SASA + CAVITY_OFFSET. Default.
> # 2: uses the solvent-accessible-surface area to correlate the
> # repulsive (cavity) term only, and uses a surface-integration
> # approach to compute the attractive (dispersion) term:
> # Gnp = Gdisp + Gcavity
> # = Gdisp + CAVITY_SURFTEN * SASA + CAVITY_OFFSET.
> # When this option is used, RADIOPT has to be set to 1,
> # i.e. the radii set optimized by Tan and Luo to mimic Gnp
> # in TIP3P explicit solvents. Otherwise, there is no guarantee
> # that Gnp matches that in explicit solvents.
> # CAVITY_SURFTEN/CAVITY_OFFSET - Values used to compute the nonpolar
> # solvation free energy Gnp according NPOPT. The default values
> # are for NPOPT set to 0 and RADIOPT set to 0 (see above).
> # If NPOPT is set to 1 and RADIOPT set to 1, these two lines
> # can be removed, i.e. use the default values set in pbsa
> # for this nonpolar solvation model. Otherwise, please
> # set these to the following:
> # CAVITY_SURFTEN: 0.04356
> # CAVITY_OFFSET: -1.008
> #
> # NP Parameters for nonpolar solvation energies if MS = 1
> #
> # SURFTEN/SURFOFF - Values used to compute the nonpolar contribution Gnp
> to
> # the desolvation according to Gnp = SURFTEN * SASA + SURFOFF.
> #
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 2
> LINIT 1000
> PRBRAD 1.4
> ISTRNG 0.0
> RADIOPT 0
> NPOPT 1
> CAVITY_SURFTEN 0.0072
> CAVITY_OFFSET 0.00
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> #
> ############################################################################
> ####
> @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
> #
> ############################################################################
> #####
> @PROGRAMS
> ## Additional program executables can be defined here
> #
> #
> ############################################################################
> ####
>
> What is the problem and why are the two values not comparable? Is anything
> wrong
> with my input. I have set RADIOPT=0, NOPT-1; also kept the values of SURFTEN
> and
> SURFOFF equal. Please help.
> Thanks a lot in advance.
>
> Sincere Regards,
> Moitrayee Bhattacharyya
> Ph.D Student
> Molecular Biophysics Unit
> Indian Institute of Science
> Bangalore-560 012
>
>
> 

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