Re: AMBER: mm_pbsa Array reference error

From: Syed Tarique Moin <tarisyed.yahoo.com>
Date: Wed, 31 Jan 2007 21:19:48 -0800 (PST)

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? Loosen up...
Download and play hundreds of games for free 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.yahoo.com
tarisyed.hotmail.com
 
---------------------------------
Want to start your own business? Learn how on Yahoo! Small Business.

#
# 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
#
################################################################################

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Feb 04 2007 - 06:07:23 PST
Custom Search