I am really confused about this becuase mm_pbsa is producing an .all.out file which seems to have
all of the important information as far as results. Afterards however the mm_pbsa_statistics.pm
starts to run and searches for some parameters that it can't find, producing endless output. What
kinds of parameters is it looking for?
I would really appreciate any advice on this problem.
Holly
> I was wondering if the problem could be that I don't have delphi installed. Is this necessary?
>
> Holly Freedman
> --
> Department of Physics, University of Alberta
> Edmonton CANADA
>
> > Dear AMBER help list,
> >
> > I am running mm_pbsa on a trajectory using the input file pasted below.
> > Unfortunately the job seems to never end, and produces an enormous output file
> > (mymm_pbsad01.log). In this output file, the message
> >
> > No values for MM_ELE existing -> Skipping
> > Processing PB PBTOT
> > Doing 1 PB PBSOL
> > Doing 1 MM GAS
> >
> > is repeated over and over again in what seems like a never-ending loop.
> >
> > Can someone please advise me on this problem?
> >
> > Thanks in advance,
> > Holly Freedman
> > --
> > Department of Physics, University of Alberta
> > Edmonton CANADA
> >
> > #
> > # 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 d01
> > PATH ./
> > #
> > COMPLEX 0
> > RECEPTOR 1
> > LIGAND 0
> > #
> > COMPT XXX
> > RECPT ../../myleapdir/d01.top
> > LIGPT XXX
> > #
> > GC 1
> > AS 0
> > DC 0
> > #
> > MM 0
> > 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 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 se
> > t
> > # 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 calculat
> > ion
> > # and dielectric assignment. A value of 0 uses the cavity radii from the prm
> > top file.
> > # A value of 1 sets up optimized cavity radii at the pbsa initialization pha
> > se.
> > # The latter radii are optimized for model compounds of proteins only; use c
> > autions
> > # 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
> > REFE 0
> > INDI 1.0
> > EXDI 80.0
> > SCALE 2.0
> > LINIT 500
> > PRBRAD 1.6
> > #
> > RADIOPT 0
> > #
> > 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
> > #
> >
>
##############################################################################
> > ##
> > .MAKECRD
> > #
> > # The following parameters are passed to make_crd_hg, which extracts snapshots
> > # from trajectory files. (This section is only relevant if GC = 1 OR AS = 1 ab
> > ove.)
> > #
> > # BOX - "YES" means that periodic boundary conditions were used during MD
> > # simulation and that box information has been printed in the
> > # trajecotry files; "NO" means opposite.
> > # NTOTAL - Total number of atoms per snapshot printed in the trajectory file
> > # (including water, ions, ...).
> > # NSTART - Start structure extraction from NSTART snapshot.
> > # NSTOP - Stop structure extraction at NSTOP snapshot.
> > # NFREQ - Every NFREQ structure will be extracted from the trajectory.
> > #
> > # NUMBER_LIG_GROUPS - Number of subsequent LSTART/LSTOP combinations to
> > # extract atoms belonging to the ligand.
> > # LSTART - Number of first ligand atom in the trajectory entry.
> > # LSTOP - Number of last ligand atom in the trajectory entry.
> > # NUMBER_REC_GROUPS - Number of subsequent RSTART/RSTOP combinations to
> > # extract atoms belonging to the receptor.
> > # RSTART - Number of first receptor atom in the trajectory entry.
> > # RSTOP - Number of last receptor atom in the trajectory entry.
> > # Note: If only one molecular species is extracted, use only the receptor
> > # parameters (NUMBER_REC_GROUPS, RSTART, RSTOP).
> > #
> > BOX YES
> > NTOTAL 51
> > NSTART 1
> > NSTOP 300
> > NFREQ 100
> > #
> > NUMBER_LIG_GROUPS 0
> > #LSTART 52
> > #LSTOP 54
> > NUMBER_REC_GROUPS 1
> > RSTART 1
> > RSTOP 51
> > #
> >
>
##############################################################################
> > ##
> > #
> > .TRAJECTORY
> > #
> > # Trajectory names
> > #
> > # The following trajectories are used to extract snapshots with "make_crd_hg":
> > # Each trajectory name must be preceeded by the TRAJECTORY card.
> > # Subsequent trajectories are considered together; trajectories may be
> > # in ascii as well as in .gz format.
> > # To be able to identify the title line, it must be identical in all files.
> > #
> > TRAJECTORY ../../d01/strip.traj
> > #
> >
>
##############################################################################
> > ##
> > #
> > .PROGRAMS
> > #
> > # Program executables
> > #
> > #DELPHI /home/gohlke/src/delphi.98/exe/delphi
> > #
> >
>
##############################################################################
> > ##
> >
> >
> > -----------------------------------------------------------------------
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--
Department of Physics, University of Alberta
Edmonton CANADA
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Received on Sun Nov 05 2006 - 06:07:13 PST
