Interface charmm

Interface to the CHARMM molecular dynamics package (www.charmm.org, commercial software). The interface was developed for version c35b3, it have not been tested with other versions of CHARMM.

Besides performing the MM calculations, the interface also handles the preparation of the calculation from a PDB file. This functionality is demonstrated in the following examples. The PDB file must be in a format recognized by CHARMM and if it contains residues not included in the CHARMM forcefield, additional parameter files have to be provided.

Methods and capabilities

The interface implements following methods (specified by keyword 'method'):

All the methods support calculation of following properties:

The interface implements following atomic charge types (keyword 'atomic_charges'):

Keywords used

Keywords specific for this interface:

Other keywords used by this interface:

Examples

The following examples, along with all other files needed to run them, can be found in the directory cuby4/interfaces/charmm/examples

#===============================================================================
# CHARMM example 1: Geometry optimization of a peptide
#===============================================================================

job: optimize
# Optimization, default setup used

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

geometry: ala-ala-zwitterion.pdb
# The geometry has to be in PDB format and conform to the conventions used
# in charmm. It is strongly advised that the PDB is build by charmm.

# For simple systems, such as this dipeptide with standard termini, the PSF
# file needed for the calculation is generated automatically without any
# user input. See example 2 for handling non-standard termini of a segment and
# example 3 for calculations with PSF supplied by the user.

#-------------------------------------------------------------------------------
# Interface configuration
#-------------------------------------------------------------------------------
# (change the paths to match your installation)

# Charmm executable
charmm_exe: /home/rezac/bin/charmm35/c35b3/exec/gnu/charmm
# Path(s) to parameter files
charmm_ff_paths:
  - /home/rezac/bin/charmm35/c35b3/toppar

# Forcefield to be used
charmm_ff_top: top_all27_prot_na.rtf
charmm_ff_par: par_all27_prot_na.prm


#===============================================================================
# CHARMM example 2: Patches for peptide chain termini
#===============================================================================

job: energy
interface: charmm

geometry: ace-ala-nme.pdb
# Alanine with acetyl and N-methyl termini.

# To generate the PSF file for such a system, it is necessary to instruct charmm
# how to patch the termini. This is done for each segment of the PDB separately.
# In this case, there is only one segment named PEP1:
charmm_segment_end_patches:
  PEP1: ACED, CT3


#-------------------------------------------------------------------------------
# Interface configuration
#-------------------------------------------------------------------------------
# (change the paths to match your installation)

# Charmm executable
charmm_exe: /home/rezac/bin/charmm35/c35b3/exec/gnu/charmm
# Path(s) to parameter files
charmm_ff_paths:
  - /home/rezac/bin/charmm35/c35b3/toppar

# Forcefield to be used
charmm_ff_top: top_all27_prot_na.rtf
charmm_ff_par: par_all27_prot_na.prm

#===============================================================================
# CHARMM example 3: Calculation using an existing PSF file
#===============================================================================

job: energy
interface: charmm

geometry: ace-ala-nme.pdb
# Alanine with acetyl and N-methyl termini, same as in example 2

# To avoid the need for generation of the PSF file, for which additional setup
# might be needed, it is possible to specify an already prepared PSF file:
charmm_psf_file: ace-ala-nme.psf 

#-------------------------------------------------------------------------------
# Interface configuration
#-------------------------------------------------------------------------------
# (change the paths to match your installation)

charmm_exe: /Users/honza/bin/CHARMM/c35b3/exec/gnu/charmm
# Charmm executable

charmm_ff_top: /Users/honza/bin/CHARMM/c35b3/toppar/top_all27_prot_na.rtf
charmm_ff_par: /Users/honza/bin/CHARMM/c35b3/toppar/par_all27_prot_na.prm
# Forcefield to be used