Re: AMBER: mm_pbsa Array reference error

From: Syed Tarique Moin <tarisyed.yahoo.com>
Date: Sat, 3 Feb 2007 21:51:27 -0800 (PST)

Scott,

Kindly fix it and give me a detail correction that you would.

Syed

Scott Pendley <scott.pendley.gmail.com> wrote: 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?
>
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> >
> >
> >
> >
> > 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



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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>




 


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
 
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