Hi,
Sorry. I left the section with the input of the NM part. Now it works.
Best regards,
Hannes
>
>
> Hi,
>
> I make a MM_PB/GBSA analysis of a protein ligand complex. I performed a
> calculation without normal mode analysis and it worked fine. But if i use the
> same input file and switch nmode to 1 i get the error: Param DIELC does not
> exist. This parameter is set to 1.0 in the MM part of the input file. What's
> the problem? I attached the mmpbsa input file and the log file.
>
> Best regards,
> Hannes Wallnoefer
>
> input file:
> .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).
> # 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 ./SNAPSHOTS/
> #
> COMPLEX 1
> RECEPTOR 2
> LIGAND 1
> #
> COMPT ./../COM.prmtop
> RECPT ./../REC.prmtop
> LIGPT ./../LIG.prmtop
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 1
> PB 1
> MS 1
> #
> NM 1
> #
>
################################################################################
> .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
> #
> #
>
################################################################################
> =>> Init data
> Presuming executables of amber suite to be in /apps/prod/amber/amber/exe
>
> =>> Reading input parameters
> Found PREFIX => snapshot
> Found PATH => ./SNAPSHOTS/
> Found COMPLEX => 1
> Found RECEPTOR => 1
> Found LIGAND => 1
> Found COMPT => ./../COM.prmtop
> Found RECPT => ./../REC.prmtop
> Found LIGPT => ./../LIG.prmtop
> Found GC => 0
> Found AS => 0
> Found DC => 0
> Found MM => 1
> Found GB => 1
> Found PB => 1
> Found MS => 1
> Found NM => 1
> Found PROC => 2
> Found REFE => 0
> Found INDI => 1.0
> Found EXDI => 80.0
> Found SCALE => 2
> Found LINIT => 1000
> Found PRBRAD => 1.4
> Found ISTRNG => 0.0
> Found RADIOPT => 0
> Found NPOPT => 1
> Found CAVITY_SURFTEN => 0.0072
> Found CAVITY_OFFSET => 0.00
> Found SURFTEN => 0.0072
> Found SURFOFF => 0.00
> Found DIELC => 1.0
> Found IGB => 2
> Found GBSA => 1
> Found SALTCON => 0.00
> Found EXTDIEL => 80.0
> Found INTDIEL => 1.0
> Found SURFTEN => 0.0072
> Found SURFOFF => 0.00
> Found PROBE => 0.0
>
> =>> Checking sanity
> Checking GENERAL
> Checking MM
> Checking NM
>
> log-file:
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Apr 18 2008 - 21:20:17 PDT
