AMBER Archive (2007)

Subject: Re: AMBER: mm_pbsa Array reference error

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Thu Feb 01 2007 - 11:05:27 CST

Ok, first GC = 0, means you turned off the command to generate snapshots. I
am going to assume that this is intentional. Can you send me a list of the
current directory that you are running this in so I can see the snapshot you
are trying to run this with.

Scott

On 1/31/07, Syed Tarique Moin <tarisyed_at_yahoo.com> wrote:
>
> Scott,
>
> I am sending you input file, if it is solved so kindly give me detail
> correction of my input file, if possible.
>
> Regards
>
>
> *Scott Pendley <scott.pendley_at_gmail.com>* wrote:
>
> Syed,
>
> This questions has been asked many times and a quick search of the
> archives should have helped you out immensely. I have only seen this error
> when eithor 1) I forget to create snapshots and then try to conduct mm_pbsa
> on a lack of snapshots or 2) the name of the snapshots does not match the
> name specificied in the input file for the mm_pbsa.pl. If this is not the
> case, please send me your input file and I can help you trouble shoot it.
>
> Scott
>
> On 1/27/07, Syed Tarique Moin <tarisyed_at_yahoo.com> wrote:
> >
> > Hello,
> >
> > Anyone can suggest me a solution for the following error that i am
> > facing to run mm_pbsa.pl.
> >
> > Can't use an undefined value as an ARRAY reference at
> > /usr/local/amber8/src/mm_pbsa/mm_pbsa_statistics.pm
> > line 903
> >
> > I want assistance to solve it.
> >
> > Regards
> >
> > Syed Tarique Moin,
> > Junior Research Fellow,
> > H.E.J. Research Institute of Chemistry,
> > International Center for Chemical and Biological Sciences,
> > University of Karachi, Karachi-75720, Pakistan
> >
> > tarisyed_at_yahoo.com
> > tarisyed_at_hotmail.com
> > ------------------------------
> > Bored stiff? <http://us.rd.yahoo.com/evt=49935/*http://games.yahoo.com>Loosen up...
> > Download and play hundreds of games for free<http://us.rd.yahoo.com/evt=49935/*http://games.yahoo.com>on Yahoo! Games.
> >
>
>
>
>
> Syed Tarique Moin,
> Junior Research Fellow,
> H.E.J. Research Institute of Chemistry,
> International Center for Chemical and Biological Sciences,
> University of Karachi, Karachi-75720, Pakistan
>
> tarisyed_at_yahoo.com
> tarisyed_at_hotmail.com
>
> ------------------------------
> Want to start your own business? Learn how on Yahoo! Small Business.<http://us.rd.yahoo.com/evt=41244/*http://smallbusiness.yahoo.com/r-index>--0-1001657078-1170307188=:91121--
>
>
> #
> # 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 a PB method (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 snapshot
> PATH ./
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ./ras_raf_II_wt.prmtop
> RECPT ./ras_II_wt.prmtop
> LIGPT ./raf_wt.prmtop
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 1
> PB 1
> MS 1
> #
> NM 0
> #
>
> ################################################################################
> @DECOMP
> #
> # Energy decomposition parameters (this section is only relevant if DC = 1
> above)
> #
> # Energy decomposition is performed for gasphase energies, desolvation
> free
> # energies calculated with GB, and nonpolar contributions to
> desolvation
> # using the LCPO method.
> # For amino acids, decomposition is also performed with respect to
> backbone
> # and sidechain atoms.
> #
> # DCTYPE - Values of 1 or 2 yield a decomposition on a per-residue
> basis,
> # values of 3 or 4 yield a decomposition on a pairwise
> per-residue
> # basis. For the latter, so far the number of pairs must not
> # exceed the number of residues in the molecule considered.
> # Values 1 or 3 add 1-4 interactions to bond contributions.
> # Values 2 or 4 add 1-4 interactions to either electrostatic or
> vdW
> # contributions.
> #
> # COMREC - Residues belonging to the receptor molecule IN THE COMPLEX.
> # COMLIG - Residues belonging to the ligand molecule IN THE COMPLEX.
> # RECRES - Residues in the receptor molecule.
> # LIGRES - Residues in the ligand molecule.
> # {COM,REC,LIG}PRI - Residues considered for output.
> # {REC,LIG}MAP - Residues in the complex which are equivalent to the
> residues
> # in the receptor molecule or the ligand molecule.
> #
> DCTYPE 2
> #
> COMREC 1-166 254-255
> COMLIG 167-253
> COMPRI 1-255
> RECRES 1-168
> RECPRI 1-168
> RECMAP 1-166 254-255
> LIGRES 1-87
> LIGPRI 1-87
> LIGMAP 167-253
>
> ################################################################################
> @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 cavity 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 caution 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
> LINIT 1000
> 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) and 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
> #
> # Parameters for sander/nmode calculation (this section is only relevant
> if NM = 1 above)
> #
> # The following parameters are passed to sander (for minimization) and
> nmode
> # (for entropy calculation using gasphase statistical mechanics).
> # For further details see documentation.
> #
> # DIELC - (Distance-dependent) dielectric constant
> # MAXCYC - Maximum number of cycles of minimization.
> # DRMS - Convergence criterion for the energy gradient.
> #
> DIELC 4
> MAXCYC 10000
> DRMS 0.0001
> #
>
> #################################################################################
> @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 above.)
> #
> # 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 25570
> NSTART 1
> NSTOP 5000
> NFREQ 500
> #
> NUMBER_LIG_GROUPS 0
> LSTART 0
> LSTOP 0
> NUMBER_REC_GROUPS 1
> RSTART 1
> RSTOP 2666
> #
>
> #################################################################################
> @ALASCAN
> #
> # The following parameters are additionally passed to make_crd_hg in
> conjunction
> # with the ones from the @MAKECRD section if "alanine scanning" is
> requested.
> # (This section is only relevant if AS = 1 above.)
> #
> # The description of the parameters is taken from Irina Massova.
> #
> # NUMBER_MUTANT_GROUPS - Total number of mutated residues. For each
> mutated
> # residue, the following four parameters must be
> given
> # subsequently.
> # MUTANT_ATOM1 - If residue is mutated to Ala then this is a pointer on
> CG
> # atom of the mutated residue for all residues except
> Thr,
> # Ile and Val.
> # A pointer to CG2 if Thr, Ile or Val residue is mutated
> to Ala
> # A pointer to OG if Ser residue is mutated to Ala
> # If residue is mutated to Gly then this is a pointer on
> CB.
> # MUTANT_ATOM2 - If residue is mutated to Ala then this should be zero
> for
> # all mutated residues except Thr, VAL, and ILE.
> # A pointer on OG1 if Thr residue is mutated to Ala.
> # A pointer on CG1 if VAL or ILE residue is mutated to
> Ala.
> # If residue is mutated to Gly then this should be always
> zero.
> # MUTANT_KEEP - A pointer on C atom (carbonyl atom) for the mutated
> residue.
> # MUTANT_REFERENCE - If residue is mutated to Ala then this is a pointer
> on
> # CB atom for the mutated residue.
> # If residue is mutated to Gly then this is a pointer
> on
> # CA atom for the mutated residue.
> # Note: The method will not work for a smaller residue mutation to a
> bigger
> # for example Gly -> Ala mutation.
> # Note: Maximum number of the simultaneously mutated residues is 40.
> #
> NUMBER_MUTANT_GROUPS 3
> MUTANT_ATOM1 1480
> MUTANT_ATOM2 0
> MUTANT_KEEP 1486
> MUTANT_REFERENCE 1477
> MUTANT_ATOM2 1498
> MUTANT_ATOM1 1494
> MUTANT_KEEP 1500
> MUTANT_REFERENCE 1492
> MUTANT_ATOM1 1552
> MUTANT_ATOM2 0
> MUTANT_KEEP 1562
> MUTANT_REFERENCE 1549
> #
>
> #################################################################################
> @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 ../prod_II/md_nvt_prod_pme_01.mdcrd.gz
> TRAJECTORY ../prod_II/md_nvt_prod_pme_02.mdcrd.gz
> TRAJECTORY ../prod_II/md_nvt_prod_pme_03.mdcrd.gz
> TRAJECTORY ../prod_II/md_nvt_prod_pme_04.mdcrd.gz
> TRAJECTORY ../prod_II/md_nvt_prod_pme_05.mdcrd.gz
> #
>
> ################################################################################
> @PROGRAMS
> #
> # Program executables
> #
> # DELPHI /home/gohlke/src/delphi.98/exe.R10000/delphi
> #
>
> ################################################################################
>
>

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