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--
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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Received on Sun Nov 05 2006 - 06:07:11 PST