Interface amber

#===============================================================================
# Amber example 1: simplest energy calculation
#===============================================================================

# Forcefield energy calculation of a small protein

job: energy

interface: amber
# Note: method does not have to be specified,
# the interface do not implement more methods

geometry: trpcage.pdb
# The tryptofan cage miniprotein.
# The geometry has to be in PDB format

#-------------------------------------------------------------------------------
# Interface configuration
#-------------------------------------------------------------------------------
# The path to amber has to be specified. This should be the base directory
# of the amber installation (when the amber environment is set up, this path
# can be found in $AMBERHOME).
# This configuration is usually done not in the input file, but in a config file
# ~/cuby4_config.yaml

amber_amberhome: /home/rezac/bin/amber/amber11/arch/amd64-intel_11.0.081/amber11
# Provide the actual path on your system here


#-------------------------------------------------------------------------------
# Defaults assumed
#-------------------------------------------------------------------------------
# The input is so simple because it uses default values for several keywords
# needed for the calculations. For this interface, these are:

# amber_leaprc: ["$AMBERHOME/dat/leap/cmd/leaprc.ff03.r1", "$AMBERHOME/dat/leap/cmd/leaprc.gaff"]
# a path(s) to one or more leaprc files, which are used to generate the
# forcefield parameters and molecule topology (the prmtop file) from the geometry
# in PDB format. By default, the ff03 and gaff forcefields are loaded
# from the amber innstallation dir specified by amber_amberhome.

# amber_top_file (not set)
# when this keyword is not set, cuby generates the prmtop file automatically

# amber_input_file (not set)
# when this keyword is not set, cuby generates the input for the calculation

# amber_sander_exe: "$AMBERHOME/bin/sander"
# by default, the sander executable (which runs the actual calculation) from
# the amber directory (specified by amber_amberhome) is used

# amber_ld_path: ""
# when the amber binaries depend on libraries that can not be found automatically,
# specify the path to them here and it is appended to the LD_LIBRARY_PATH
# environment variable before amber is run

#===============================================================================
# Amber example 2: Geometry optimization
#===============================================================================

# Geometry optimization of a peptide using an user-specified forcefield

# This example assumes that the interface is already configured, and uses some
# default values - see example 1 for reference. 

job: optimize
interface: amber
geometry: ace-ala-nme.pdb

amber_leaprc: $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
# We use another forcefiled available in amber, defined in this file
# (This one is older than the ff03 forcefield used by default)
# For newer versions of amber, use the following:
# amber_leaprc: $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff99SB

# The calculation creates two files:
# history_amber_example_02.xyz - contains all the geometries along the optimization
# optimized.xyz - the optimized structure

#===============================================================================
# Amber example 3: Getting atomic charges
#===============================================================================

# The interface can be used to extract atomic charges from the forcefield
# for the calculated system. The input is the same as for a real calculation
# of the charges by other methods.

job: atomic_charges
interface: amber
geometry: ../02/ace-ala-nme.pdb

atomic_charges: forcefield
# The type of the charges must be provided, in this case "forcefield" is
# the only option.

#===============================================================================
# Amber example 4: Solvation
#===============================================================================

# In this example, solvation energy is calculated as a difference between
# a calculation using implicit solvent and another gas phase calculation.
# To get the result from a single cuby job, composite interface mixer is
# used to run both calculations in parallel and subtract the results.

job: energy
interface: mixer

geometry: ../02/ace-ala-nme.pdb

print: energy_decomposition
# print components of the final energy, in this case energies of the two
# separate calculation (optional)

cuby_threads: 2
# run the two separate calculation in parallel (optional)

mixer_weight_a:  1.0
mixer_weight_b: -1.0
# This defines the weights (wA, wB) of the calculations, the resulting energy
# is then E = wA * E(A) + wB * E(B)

# The two calculations are defined as separate blocks of the input (the block
# name comes first, the contents of the block are then indented).

calculation_a: # Calculation in implicit solvent (GBM)
  interface: amber
  solvent_model: gbm
  # here, the solvent model is defined, the possible options are gbm and igb7
  # dilelectric constant can be specified by keyword solvent_epsilon,
  # the value of 78.5 (water) is used by default

calculation_b:
  interface: amber
  # amber calculation, everything set to default

#===============================================================================
# Amber example 5: Using a user-modified forcefield
#===============================================================================

# Geometry optimization of a peptide using an forcefield with a new
# residue defined by the user

# This example assumes that the interface is already configured, and uses some
# default values - see example 1 for reference. 

job: energy
interface: amber

geometry: peptide-fma.pdb
# The geometry contains a residue not defined in the forcefield - formic acid,
# residue name 'fma'

amber_leaprc: leaprc.my # use leaprc.new if you have newer version of amber
# We use a custom leaprc file that
# 1) loads the amber forcefield for the peptide part
# 2) loads the gaff forcefield for general organic molecules
# 3) adds parameters missing in the gaff forcefileld - the frcmod file
# 4) loads the template for the 'fma' residue - a mol2 file
#    this file also contains the atomic charges for this molecule


# AN IMPORTANT FEATURE is used here: every leaprc file is preprocessed
# by cuby and following patterns are replaced with actual paths:
# %amberhome (path to amber installation)
# %home (path to home directory)
# %cuby (path to cuby inctallation)
# %pwd (path curernt working directory)
# This allows easy construction of portable leaprc files combining
# data from different sources.

# The parameters for an unknown molecule can be generated by the
# antechamber program packaged with AMBER, see the documentation for more
# information.

#===============================================================================
# Amber example 6: Use of external point charges
#===============================================================================

# Geometry optimization of a water molecule in external electric field created
# by two point charges along the x axis. In the optimization, the molecule
# aligns with the field.

job: optimize
interface: amber

geometry: water.pdb

remove_translation: yes
remove_rotation: no
# Allow rotation, by default both translational and rotational components of
# the gradient are removed.

point_charges: |
  10.0  0.0 0.0   1.0
  -10.0 0.0 0.0  -1.0
# A list of point charges, four numbers (x, y, z, charge) per line.