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MCCCS Towhee (input_style 'advanced connectivity map')

 

 

This section describes the input variables associated with an input_style setting of 'advanced connectivity map'. This option adds additional flexibility compared to the similar basic connectivity map and is designed to replace that option. This documentation is only maintained for the current version of the code. This molecule assembly option is a powerful and relatively easy way to set up the molecular interactions by listing the atom types and providing their bond partners and rudimentary information about the bond orders. This option is designed to work with the force fields and atom names listed in the Towhee Capabilities section. This option determines all of the vibration types, bending angles, bending types, regular torsion angles, regular torsion types, angle-angle terms, angle-angle types, and improper torsion types that are implied by the bonding structure of the molecule. It also provides an option for a rule-based determination of improper torsions based upon the bonding pattern.

 

nunit (integer)
  • The number of atoms (or united-atoms) in this molecule. Must be less than or equal to NUMAX (see preproc.h).
nmaxcbmc (integer)
  • The maximum number of atoms to regrow during a configurational-bias regrowth. It is suggested to set this to the same value as nunit, but some molecules are so large that almost none of the moves which regrow large portions are accepted. In those cases setting a lower value of nmaxcbmc focused the software on moves that are likely to be accepted.
lpdbnames (logical)
  • .TRUE. : to enable the input of information about the pdb (protein data bank) atom name, amino acid number, amino acid name. This information is needed in order to use the cartoon feature of certain pdb viewers (such as Rasmol).
  • .FALSE. : to disable the input of additional pdb information. This does not disable the output of pdb files, it just means thing like the Rasmol cartoon feature will not work properly.
forcefield (character*10)
  • The Towhee shorthand name for the forcefield that you want to use to build this molecule. See Towhee Capabilities for a complete list of the forcefields included with the Towhee distribution.
charge_assignment (character*30)
  • 'bond increment': the bond increment method is used to assign the charges on each atom and the variable charge is not required. Note that this method is not functional for all forcefields.
  • 'manual': the charges on each atom are manually specified in the towhee_input file as the variable charge in the following section.
  • 'none': a zero charge is assigned to each atom and the variable charge is not required.
improper_assignment (character*30)
  • '3-bond: single improper': atoms that are bonded to exactly three neighbors are assigned a single improper torsions automatically. The three neighbors are automatically assigned in increasing order of their nonbonded integer type number. Originally implemented for use with the MMFF94 force field. The improper torsion variables are not required in the subsequent section.
  • 'manual': the improper torsions each atom are manually specified in the subsequent section.
  • 'none': no improper torsions are assigned for this molecule and the improper torsion variables are not required in the subsequent section.
match_style (character*30)
  • 'standard' : determines matching interactions for a given forcefield by checking for exact type matches first, and then utilizing a procedure that checks for an increasing number of wildcards. This is the approach recommended for the majority of forcefields and is the default value used by most of the other molecule assembly options.
  • 'stereoselective' : very similar to the 'standard' option, but also requires the input of a list of torsions that have a specific stereochemistry. This allows the process to distinguish between cis and trans dihedrals when combined with a forcefield that makes such a distinction. When using this option the special_torsion_count variables are required after the usual input of the connectivity.
  • 'MMFF checkdown' : determines matching interactions for a given forcefield using the procedure described in the MMFF94 forcefield papers. This uses an internal checkdown procedure based upon atom names that are implemented as a 10 character string that contains 5 2-character substrings.

 


The variables in this section are required for each atom in the molecule (determined by nunit), one atom at a time.
unit (integer), type (character), charge (double precision)
  • unit is the number of the atom in order starting from atom number 1.
  • ntype is the character string that contains the atom type for this atom. Information about valid atomtypes is found in individual forcefield documentation (see the Towhee Capabilities manual).
  • charge is the charge on this atom. This is only required if the charge_assignment variable is set to 'manual'.
pdbname (character), aminonum (integer), aminoshort (character)
    Note: These variables are only listed if lpdbnames = .TRUE.
  • pdbname: A four character string that is output in the pdb file. The precise spacing is important if you want most pdb viewers to recognize the atoms as the pdb file is extremely specific.
  • aminonum: The number of each amino acid starting from the N-terminus.
  • aminoshort: The three letter code for each amino acid, or other group (such as caps on the C or N termini).
vibration
  • The first line under the vibration heading is the number of atoms that are bonded to the current atom. Must be a number between 0 and NNBOND (see preproc.h).
  • For each vibration a subsequent line contains the atom number (integer) of the bond partner and the vibration order (character string a10) of the bond. Commonly used vibration orders are listed here.
    • 'any': matches any bond order listed in the force field file. This effectively disables the vibration order searching. This entry is only valid in the towhee_input file, and not in an ff*.F file.
    • 'aromatic': aromatic bond
    • 'single': single bond
    • 'double': double bond
    • 'triple': triple bond
    • 'wild': matches with any type of bond, but only if there is not an exact match. This is only a valid entry in an ff*.F file, and not in the towhee_input file.
improper torsion
    Note: These variables are only listed for certain settings of improper_assignment
  • The first line under the improper heading is the number of improper torsions (any form) that have the central atom located at the current atom. You must list all improper torsions that have the current atom at the central position, but you do not list improper torsions that only contain the current atom at one of the ends. Must be a number between 0 and MAXIMPROP (see preproc.h).
  • For each improper torsion specified above a line with the following information is required. A list of the three other atoms in the improper torsion followed by the appropriate improper type for the force field. The code currently only allows an improper torsion where the three other atoms are all bonded to the first atom. If you want to enable the automatic determination of the improper torsion force field parameters then set the improper force field type to 0.
This is the end of the section that is repeated for each atom
special_torsion_count
    Note: These variables are only listed for certain settings of match_style
  • The first line under the special_torsion_count heading is the number of special torsion assignments that involve a torsion order other than 'wild'. If this value is not 0, then a subsequent line is required for each value of this variable.
  • For each value of the special_torsion_count specified above, a line with the following information is required. A list of the integer values of the 4 atoms that make up the special torsion, followed by a character string that describes the special torsion. The character string is checked against the torsion order specified in the various forcefield files in order to determine a match. The torsions only need to be specified in a single order, so if there was a special torsion between atoms 1,2,3, and 4 it is only required to list the 1 2 3 4 'special flag' direction and not the 4 3 2 1 'special flag' direction. The special torsion order character string depends upon the force field, but typical values are listed here.
    • 'wild' : default value if none is specified. This matches up with torsions that do not have a specified torsion order as the default output for the torsion order is 'wild'. There is no reason to go through the effort of listing this value since it is the default, but it would result in a valid match with the default torsions so it is allowed.
    • 'cis' : matches up with a torsion that is in the cis conformation only. Typically occurs for double bonded carbons that are then bonded to dissimilar atoms.
    • 'trans' : matches up with a torsion that is in the trans conformation only. Typically occurs for double bonded carbons that are then bonded to dissimilar atoms.

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Send comments to: Marcus G. Martin

Last updated:August 11, 2014