Dear all,
recently I wanted to do MM/PBSA analysis of my system using mm_pbsa.pl
script (AmberTools 1.4)
using INP=2 as it is recommended for case of branched and cyclic molecules
in Amber manual.
As recommended for this choice I also set RADIOPT=1.
Unfortunately calculation crashed with this error:
PB Bomb in pb_aaradi(): No radius assigned for atom 616 C4 CG
when I tried to use RADIOPT=0 to force reading atom radii from PRMTOP
file, it crashed immediately
with no error message written in any output file.
It seems that RADIOPT=1 is really mandatory for INP=2.
My interpretation of the above error is that Tan & Luo radius for Glycam
atom type "CG" is
unknown. If I am right I just don.t understand why in such case atom
radius from PRMTOP file
is not automatically used like in case of GAFF ( lowercase ) forcefield.
I would be grateful for any useful advice here (To change all CG to CT in
prmtop file (just for PB calculation) ? or to add some lines in relevant
Amber source file ? ...).
Thanks in advance !
Best wishes,
Marek
Here is for completnes relevant part of my MM/PBSA input file:
#
# Input parameters for mm_pbsa.pl
#
# Holger Gohlke
# 25.02.2010
#
################################################################################
.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).
#
# VERBOSE - If set to 1, input and output files are not removed. This is
useful for
# debugging purposes.
# PARALLEL - If set to values > 1, energy calculations for snapshots are
done
# in parallel, using PARALLEL number of threads.
#
# 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.
# START - Specifies the first snapshot to be used in energy calculations
(optional, defaults to 1).
# STOP - Specifies the last snapshot to be used in energy calculations
(optional, defaults to 10e10).
# OFFSET - Specifies the offset between snapshots in energy calculations
(optional, defaults to 1).
#
# 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 INP 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 INP option in pbsa (see below).
# NM - Calculation of entropies with nmode.
#
VERBOSE 0
PARALLEL 2
#
PREFIX snap
PATH ../0_snaps
START 399
STOP 400
OFFSET 1
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../prmtop/com.prmtop
RECPT ../prmtop/rec.prmtop
LIGPT ../prmtop/lig.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 0
PB 1
MS 0
#
NM 0
#
################################################################################
.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.
# IVCAP - If set to 1, a solvent sphere (specified by CUTCAP,XCAP,YCAP,
# and ZCAP) is excised from a box of water. If set to 5, a
solvent shell
# is excised, specified by CUTCAP (the thickness of the shell in
A).
# The electrostatic part
# of the solvation free energy is estimated from a linear
response
# approximation using the explicit water plus a reaction field
# contribution from outside the sphere (i.e., a hybrid solvation
approach
# is pursued). In addition, the nonpolar
# contribution is estimated from a sum of (attractive) dispersion
# interactions calc. between the solute and the solvent molecules
# plus a (repulsive) cavity contribution. For the latter,
# the surface calculation must be done with MS = 1 and the PROBE
should
# be set to 1.4 to get the solvent excluded surface.
# CUTCAP - Radius of the water sphere or thickness of the water shell.
# Note that the sphere must enclose the whole solute.
# XCAP - Location of the center of the water sphere.
# YCAP
# ZCAP
#
# NP Parameters for nonpolar solvation energies if MS = 0
#
# INP - 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 = SURFTEN * SASA + SURFOFF. 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 + SURFTEN * SASA + SURFOFF.
# 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.
# SURFTEN/SURFOFF - Values used to compute the nonpolar
# solvation free energy Gnp acccording to INP.
# If INP = 1 and RADIOPT = 0 (default, see above),
# use SURFTEN/SURFOFF parameters that fit with the radii from the
# prmtop file, e.g., use SURFTEN: 0.00542; SURFOFF: 0.92 for
PARSE radii.
# If INP = 2 and RADIOPT = 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: SURFTEN: 0.04356; 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 either
# (I) Gnp = SURFTEN * SASA + SURFOFF (if IVCAP = 0) or
# (II) Gnp = Gdisp + Gcavity = Gdisp + SURFTEN * SESA + SURFOFF
(if IVCAP > 0).
# In the case of (I), use parameters that fit with the radii
from the
# reaction field calculation. E.g., use SURFTEN: 0.00542,
SURFOFF: 0.92
# for PARSE radii or use SURFTEN: 0.005, SURFOFF: 0.86 for Tan &
Luo radii.
# In the case of (II), use SURFTEN: 0.069; SURFOFF: 0.00 for
calculating the
# Gcavity contribution.
#
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 3
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 1
INP 2
#
#SURFTEN 0.00542
#SURFOFF 0.92
#
IVCAP 0
CUTCAP -1.0
XCAP 0.0
YCAP 0.0
ZCAP 0.0
#
################################################################################
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Received on Tue Mar 15 2011 - 21:30:02 PDT
