Syed,
According to your input file, you do NOT want to generate snapshots (GC 0),
and snapshots are labeled snapshot_rec.crd.X (PREFIX snapshot) and are
located in your current directory (PATH ./). According to your directory
listing this is not correct. I would fix this.
Scott
On 2/1/07, Syed Tarique Moin <tarisyed.yahoo.com> wrote:
>
> Hi Scott
>
> I am sending you the list of the files in the
> directory.
>
> Thanks in advance
>
> --- Scott Pendley <scott.pendley.gmail.com> wrote:
>
> > 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.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.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.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.yahoo.com
> > > > tarisyed.hotmail.com
> > > > ------------------------------
> > > > Bored stiff?
> >
> <http://us.rd.yahoo.com/evt=49935/*http://games.yahoo.com>Loosen
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> > 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.yahoo.com
> > > tarisyed.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
> > > #
> > >
> > >
> >
>
> ################################################################################
> > >
> > >
> >
>
> 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.yahoo.com
> tarisyed.hotmail.com
>
>
>
>
> ____________________________________________________________________________________
> Do you Yahoo!?
> Everyone is raving about the all-new Yahoo! Mail beta.
> http://new.mail.yahoo.com
> total 3556
> drwxr-xr-x 8 zuh users 4096 2007-01-26 11:42 Examples
> -rw-r--r-- 1 zuh users 23273 2007-01-25 12:26 _make_crd_hg.f
> -rw-r--r-- 1 zuh users 23312 2007-01-25 12:26 make_crd_hg.f
> -rw-r--r-- 1 zuh users 49492 2007-01-25 12:26 make_crd_hg.o
> -rw-r--r-- 1 zuh users 1894 2007-01-25 12:26 Makefile
> -rw-r--r-- 1 zuh users 16458 2007-01-25 12:26 mm_pbsa_calceneent.pm
> -rw-r--r-- 1 zuh users 1650 2007-01-25 12:26 mm_pbsa_createcoords.pm
> -rw-r--r-- 1 zuh users 16175 2007-01-25 12:26 mm_pbsa_createinput.pm
> -rw-r--r-- 1 zuh users 2677 2007-01-25 12:26 mm_pbsa_global.pm
> -rw-r--r-- 1 zuh users 14215 2007-01-26 12:16 mm_pbsa.in
> -rw-r--r-- 1 zuh users 3369 2007-01-26 12:27 mm_pbsa.log
> -rw-r--r-- 1 zuh users 992 2007-01-25 12:26 mm_pbsa_output.txt
> -rwxr-xr-x 1 zuh users 2146 2007-01-25 12:26 mm_pbsa.pl
> -rw-r--r-- 1 zuh users 15961 2007-01-26 11:55 mm_pbsa_readinput.pm
> -rwxr-xr-x 1 zuh users 1036 2007-01-25 12:26 mm_pbsa_statistics.pl
> -rwxr-xr-x 1 zuh users 54083 2007-01-25 12:26 mm_pbsa_statistics.pm
> -rw-r--r-- 1 zuh users 2183 2007-01-25 12:26 mm_pbsa_util.pm
> -rw-r--r-- 1 zuh users 241256 2007-01-25 12:26 molsurf.c
> -rw-r--r-- 1 zuh users 10140 2007-01-25 12:26 molsurf.h
> -rw-r--r-- 1 zuh users 101324 2007-01-25 12:26 molsurf.o
> drwxr-xr-x 2 zuh users 4096 2007-01-27 15:22 new
> -rw-r--r-- 1 zuh users 383 2007-01-31 15:18 pbsa.in
> -rw-r--r-- 1 zuh users 475632 2007-01-26 11:29 raf_wt.prmtop
> -rw-r--r-- 1 zuh users 1004670 2007-01-26 11:29 ras_II_wt.prmtop
> -rw-r--r-- 1 zuh users 1464057 2007-01-26 11:29 ras_raf_II_wt.prmtop
> -rw-r--r-- 1 zuh users 365 2007-01-31 15:18 sander_com.in
> -rw-r--r-- 1 zuh users 365 2007-01-31 15:18 sander_lig.in
> -rw-r--r-- 1 zuh users 365 2007-01-31 15:18 sander_rec.in
> -rw-r--r-- 1 zuh users 12 2007-01-31 15:18 snapshot_com.all.out
> -rw-r--r-- 1 zuh users 12 2007-01-31 15:18 snapshot_lig.all.out
> -rw-r--r-- 1 zuh users 12 2007-01-31 15:18 snapshot_rec.all.out
> -rw-r--r-- 1 zuh users 63 2007-01-31 15:18 snapshot_statistics.in
> zuh.mcg09:~/Working/Tari/Tutorial7/mm_pbsa>
>
>
>
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Received on Sun Feb 04 2007 - 06:07:58 PST
