AMBER Archive (2007)

Subject: Re: AMBER: mm_pbsa Array reference error

From: Syed Tarique Moin (tarisyed_at_yahoo.com)
Date: Wed Jan 31 2007 - 23:19:48 CST

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
---------------------------------
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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_at_yahoo.com
tarisyed_at_hotmail.com
 
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#
# 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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