AMBER Archive (2008)

Subject: AMBER: nmode problem

From: Hannes Wallnoefer (Hannes.Wallnoefer_at_uibk.ac.at)
Date: Fri Apr 18 2008 - 04:01:27 CDT

Hi,

I make a MM_PB/GBSA analysis of a protein ligand complex. I performed a
calculation without normal mode analysis and it worked fine. But if i use the
same input file and switch nmode to 1 i get the error: Param DIELC does not
exist. This parameter is set to 1.0 in the MM part of the input file. What's
the problem? I attached the mmpbsa input file and the log file.

Best regards,
Hannes Wallnoefer

input file:
@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).
# Calculation of nonpolar solvation free energies according to
# the NPOPT option in pbsa (see below).
# MS - Calculation of nonpolar contributions to desolvation using molsurf
# (see below).
# If MS == 0 and GB == 1, nonpolar contributions are calculated with the
# LCPO method in sander.
# If MS == 0 and PB == 1, nonpolar contributions are calculated according
# the NPOPT option in pbsa (see below).
# NM - Calculation of entropies with nmode.
#
PREFIX snapshot
PATH ./SNAPSHOTS/
#
COMPLEX 1
RECEPTOR 2
LIGAND 1
#
COMPT ./../COM.prmtop
RECPT ./../REC.prmtop
LIGPT ./../LIG.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 1
MS 1
#
NM 1
#
################################################################################
@PB
#
# PB parameters (this section is only relevant if PB = 1 above)
#
# The following parameters are passed to the PB solver.
# Additional input parameters may also be added here. See the sander PB
# documentation for more options.
#
# PROC - Determines which method is used for solving the PB equation:
# By default, PROC = 2, the pbsa program of the AMBER suite is used.
# REFE - Determines which reference state is taken for PB calc:
# By default, REFE = 0, reaction field energy is calculated with
# EXDI/INDI. Here, INDI must agree with DIELC from MM part.
# INDI - Dielectric constant for the solute.
# EXDI - Dielectric constant for the surrounding solvent.
# ISTRNG - Ionic strength (in mM) for the Poisson-Boltzmann solvent.
# PRBRAD - Solvent probe radius in Angstrom:
# 1.4: with the radii in the prmtop files. Default.
# 1.6: with the radii optimized by Tan and Luo (In preparation).
# See RADIOPT on how to choose a cavity radii set.
# RADIOPT - Option to set up radii for PB calc:
# 0: uses the radii from the prmtop file. Default.
# 1: uses the radii optimized by Tan and Luo (In preparation)
# with respect to the reaction field energies computed
# in the TIP3P explicit solvents. Note that optimized radii
# are based on AMBER atom types (upper case) and charges.
# Radii from the prmtop files are used if the atom types
# are defined by antechamber (lower case).
# SCALE - Lattice spacing in no. of grids per Angstrom.
# LINIT - No. of iterations with linear PB equation.
#
# NP Parameters for nonpolar solvation energies if MS = 0
#
# NPOPT - Option for modeling nonpolar solvation free energy.
# See sander PB documentation for more information on the
# implementations by Tan and Luo (In preparation).
# 1: uses the solvent-accessible-surface area to correlate total
# nonpolar solvation free energy:
# Gnp = CAVITY_SURFTEN * SASA + CAVITY_OFFSET. Default.
# 2: uses the solvent-accessible-surface area to correlate the
# repulsive (cavity) term only, and uses a surface-integration
# approach to compute the attractive (dispersion) term:
# Gnp = Gdisp + Gcavity
# = Gdisp + CAVITY_SURFTEN * SASA + CAVITY_OFFSET.
# When this option is used, RADIOPT has to be set to 1,
# i.e. the radii set optimized by Tan and Luo to mimic Gnp
# in TIP3P explicit solvents. Otherwise, there is no guarantee
# that Gnp matches that in explicit solvents.
# CAVITY_SURFTEN/CAVITY_OFFSET - Values used to compute the nonpolar
# solvation free energy Gnp according NPOPT. The default values
# are for NPOPT set to 0 and RADIOPT set to 0 (see above).
# If NPOPT is set to 1 and RADIOPT set to 1, these two lines
# can be removed, i.e. use the default values set in pbsa
# for this nonpolar solvation model. Otherwise, please
# set these to the following:
# CAVITY_SURFTEN: 0.04356
# CAVITY_OFFSET: -1.008
#
# NP Parameters for nonpolar solvation energies if MS = 1
#
# 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 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
@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
#
#################################################################################
@PROGRAMS
#
# Additional program executables can be defined here
#
#
################################################################################
=>> Init data
    Presuming executables of amber suite to be in /apps/prod/amber/amber/exe

=>> Reading input parameters
    Found PREFIX => snapshot
    Found PATH => ./SNAPSHOTS/
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT => ./../COM.prmtop
    Found RECPT => ./../REC.prmtop
    Found LIGPT => ./../LIG.prmtop
    Found GC => 0
    Found AS => 0
    Found DC => 0
    Found MM => 1
    Found GB => 1
    Found PB => 1
    Found MS => 1
    Found NM => 1
    Found PROC => 2
    Found REFE => 0
    Found INDI => 1.0
    Found EXDI => 80.0
    Found SCALE => 2
    Found LINIT => 1000
    Found PRBRAD => 1.4
    Found ISTRNG => 0.0
    Found RADIOPT => 0
    Found NPOPT => 1
    Found CAVITY_SURFTEN => 0.0072
    Found CAVITY_OFFSET => 0.00
    Found SURFTEN => 0.0072
    Found SURFOFF => 0.00
    Found DIELC => 1.0
    Found IGB => 2
    Found GBSA => 1
    Found SALTCON => 0.00
    Found EXTDIEL => 80.0
    Found INTDIEL => 1.0
    Found SURFTEN => 0.0072
    Found SURFOFF => 0.00
    Found PROBE => 0.0

=>> Checking sanity
    Checking GENERAL
    Checking MM
    Checking NM

log-file:

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