AMBER Archive (2006)

Subject: AMBER: mm_pbsa does not terminate

From: Holly Freedman (freedman_at_phys.ualberta.ca)
Date: Tue Oct 31 2006 - 18:51:19 CST

Dear AMBER help list,

I am running mm_pbsa on a trajectory using the input file pasted below.
Unfortunately the job seems to never end, and produces an enormous output file
(mymm_pbsad01.log). In this output file, the message

    No values for MM_ELE existing -> Skipping
    Processing PB PBTOT
        Doing 1 PB PBSOL
        Doing 1 MM GAS

is repeated over and over again in what seems like a never-ending loop.

Can someone please advise me on this problem?

Thanks in advance,
Holly Freedman 

--
Department of Physics, University of Alberta
Edmonton CANADA

#
# 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 delphi (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                d01
PATH                  ./
#
COMPLEX               0
RECEPTOR              1
LIGAND                0
#
COMPT                 XXX
RECPT                 ../../myleapdir/d01.top
LIGPT                 XXX
#
GC                    1
AS                    0
DC                    0
#
MM                    0 
GB                    1
PB                    1
MS                    1
#
NM                    0
#
##############################################################################
##
@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 se
t
#     and 1.6 with the radii optimized by R. Luo)
#
#   Parameters for pbsa only
#
#   RADIOPT - Option to set up atomic avity radii for molecular surface calculat
ion
#     and dielectric assignment. A value of 0 uses the cavity radii from the prm
top file.
#     A value of 1 sets up optimized cavity radii at the pbsa initialization pha
se.
#     The latter radii are optimized for model compounds of proteins only; use c
autions
#     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                 2.0
LINIT                 500
PRBRAD                1.6
#
RADIOPT               0
#
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), 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
#
##############################################################################
##
@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 ab
ove.)
#
#   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                51
NSTART                1
NSTOP                 300
NFREQ                 100
#
NUMBER_LIG_GROUPS     0
#LSTART                52
#LSTOP                 54
NUMBER_REC_GROUPS     1
RSTART                1
RSTOP                 51
#
##############################################################################
##
#
@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            ../../d01/strip.traj
#
##############################################################################
##
#
@PROGRAMS
#
# Program executables
#
#DELPHI                /home/gohlke/src/delphi.98/exe/delphi
#
##############################################################################
##
 

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