Thank you for your attention.
I am using Amber9 to calculate the binding free energy by perl script mm_pbsa.pl , the error message is : Died at /usr/local/amber9/src/mm_pbsa/mm_pbsa_calceneent.pm line 498, <PDB> line 2117.
In
the window where I had put the order : tail -f calculate1aay.log , I had
this message : Calculating energy / entropy contributions
Calc contrib for ./traj1aay/prod_com.crd.1
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
No radius found for ZN 2113 in residue ZNA 108
the input file :
#
# Input parameters for mm_pbsa.pl
# This example just generates snapshots from a trajectory file
#
# 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).
# 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 prod
PATH ./traj1aay
#
COMPLEX 1
RECEPTOR 1
LIGAND 2
#
COMPT ./1aay.top
RECPT ./1aay-rec.top
LIGPT ./1aay-lig.top
GC
0
AS 0
DC 0
#
MM 1
GB 1
PB 1
MS 1
#
NM 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 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 28061
NSTART 1
NSTOP 2115
NFREQ 1
#
NUMBER_LIG_GROUPS 2
LSTART 1
LSTOP
1416
LSTART 2113
LSTOP 2115
NUMBER_REC_GROUPS 1
RSTART 1417
RSTOP 2112
#
#################################################################################
.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 ./1aay-prod1.mdcrd
TRAJECTORY ./1aay-prod2.mdcrd
TRAJECTORY ./1aay-prod3.mdcrd
TRAJECTORY ./1aay-prod4.mdcrd
#
#
################################################################################
.PROGRAMS
#
# Additional program executables can be defined here
#
#
################################################################################
.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
#
################################################################################
.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 program is used for solving the PB equation:
# Delphi (PROC == 1), PBSA (PROC == 2), or APBS (PROC == 3).
# 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.
# SCALE - Lattice spacing in no. of grids per Angstrom.
# LINIT - No. of iterations with linear PB equation.
# 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 with respect to the
# reaction field energies computed in the TIP3P explicit solvents
# (Tan & Luo, J. Phys. Chem. B, 2006, 110, 18680-18687).
# 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).
# ARCRES - Resolution (in the unit of Angstrom) of solvent accessible arcs
# 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
# solvent 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
# (Gohlke & Case, J. comput. Chem. 2004, 25, 238-250).
# 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.
# In this case bondi radii are used as cavity radii set.
# 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.
# 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.
# 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 and SURFOFF: 0.92 for PARSE radii.
# If INP = 2 and RADIOPT = 1,
please set these to the following:
# SURFTEN: 0.0378; OFFSET: -0.5692
#
# NP Parameters for nonpolar solvation energies if MS = 1
#
# SURFTEN/SURFOFF - Values used to compute the nonpolar contribution Gnp to
# the desolvation according to:
# (I) Gnp = SURFTEN * SASA + SURFOFF (if IVCAP == 0)
# Use parameters that fit with the radii from the reaction field
# calculation. E.g., use SURFTEN: 0.00542, SURFOFF: 0.92 for
# PARSE radii
# (II) Gnp = Gdisp + Gcavity = Gdisp + SURFTEN * SESA + SURFOFF (IVCAP
> 0)
# Nonpolar solvation free energy calculated as discribed for IVCAP > 0
# above. In this case use SURFTEN: 0.069; SURFOFF: 0.00 for
# calculating the Gcavity contribution.
#
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT
1000
PRBRAD 1.4
ISTRNG 65
RADIOPT 0
NPOPT 1
CAVITY_SURFTEN 0.00542
CAVITY_OFFSET 0.92
ARCRES 0.0625
INP 1
#
SURFTEN
0.00542
SURFOFF 0.92
#
IVCAP 1
CUTCAP 10
XCAP 0.0
YCAP 0.0
ZCAP 0.0
On Monday, June 2, 2014 2:26 PM, Jason Swails <jason.swails.gmail.com> wrote:
On Mon, 2014-06-02 at 04:04 -0700, Roza M wrote:
> Dear amber users,
>
>
> I am trying to calculate the binding free energy for Zif 268-DNA
> complex using MM-PBSA, but I couldn't because it gives me the
> following : " no radius found for ZN " , In which file should I write
> the radius for Zn atom?
What kind of calculation are you running?
What is your input file?
What is your exact error message?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 02 2014 - 05:30:03 PDT
