AMBER Archive (2007)

Subject: AMBER: bad atom type:F

From: Emilia Wu (emiliawu_at_dicp.ac.cn)
Date: Thu Aug 30 2007 - 07:36:14 CDT

Dear Amber Users,

     I am using MM/GBSA of amber8 to calcuate binding energy of
protein/ligand system. There is one F atom in the ligand.
Binding calculation is working fine. But I got "bad atom type:
F" when I run energy decomposition. and I have already add " "F" => 1.470 + 1.400,"
to the script of mm_pbsa_calceneent.pm according to the mail list.

here is the input file:
#
# Input parameters for mm_pbsa.pl
# This example does decompositions by residue
#
# 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 *****_***_wat
PATH ../01/
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../01/protein.prmtop
RECPT ../01/peptide.prmtop
LIGPT ../01/ligand.prmtop
#
GC 0
AS 0
DC 1
#
MM 1
GB 1
PB 0
MS 0
#
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 1-276
COMLIG 277-277
COMPRI 1-276 277-277
RECRES 1-276
RECPRI 1-276
RECMAP 1-276
LIGRES 1-1
LIGPRI 1-1
LIGMAP 277-277
#
################################################################################
@MM
#
#
# 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 2
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
@PROGRAMS
#
# Available program executables can be defined here
#
#
################################################################################

I dont know what went wrong. What should I do?

Thanks in advance.

Emilia
+-----------------------------------------------------------------------------+
| Emilia L. Wu (Ph.D. student) |
| State Key Laboratory of Molecular Reaction Dynamics, |
| Dalian Institute of Chemical Physics, |Tel:(86411)84379352 |
| Chinese Academy of Sciences |Fax:(86411)84675584 |
| Dalian 116023, P.R.China |Email:emiliawu_at_dicp.ac.cn |
+-----------------------------------------------------------------------------+

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