MCCCS Towhee (input_style 'polypeptide builder')



This section describes the input variables associated with an input_style setting of 'polypeptide builder'. Uses the polypeptide builder functionallity to set up everything for proteins from a list of the amino acids. Documentation of the currently available monomers is presented along with the forcefield information for each force field.


nunit (integer)
  • The number of monomers in this molecule. Must be less than or equal to NUMAX (see preproc.h) and there is also a check in the builder to make sure you do not exceed NUMAX with the number of atoms that all of your monomers require.
nmaxcbmc (integer)
  • The nmaxcbmc variable determines the maximum number of atoms that are regrown during a configurational-bias regrowth.
forcefield (character)
  • The forcefield that you want to use to build this molecule.
protgeom (character)
  • linear: The polypeptide will be generated starting from the N-terminus and finishing at the C-terminus. Also allows for multiple N and C terminii where the different linear polypeptides are connected by disulfide bonds.
  • cyclic: The polypeptide is cyclic so the first amino acid is bonded to the final amino acid.


The variables listed immediately below are listed as a group for each amino acid in the molecule. There is only one line of input per building block in the molecule.
pepname (unformatted character string of length 2), stereochem (unformatted character string of length 1), bondpartner (integer), terminus (unformatted character of length 1)
  • pepname is a two letter code for the building blocks of the molecule. Peptides use a code where the first letter is the one letter code for each amino acid. The second character is generally the charge state of the side chain, but has some different meanings for histidine and cysteine. The peptide codes can be found in the documentation for each force field./a>.
  • stereochem is a single letter which determines the stereochemistry of the peptide. The valid options are l (L-amino acid), d (D-amino acid) and r (racemic).
  • bondpartner is the number of the amino acid which is bonded to this amino acid through the side chain. This is only used for cysteines that have a disulfide bridge (type cs), otherwise set this value to 0. The bondpartner integers refer to the amino acids starting with the first amino acid listed in towhee_input as amino acid #1.
  • terminus is a single character string which tells the code whether this peptide is at one of the terminii, or if it is in the central part of the polypeptide. You may have multiple N and C terminii, but all C terminii must be immediately preceded by an N-terminus.
    • 'N': N-terminus. All linear polypeptides must begin with an N-terminus
    • '-': Central polypeptide (anything that isn't an N or C terminus)
    • 'C': C-terminus. All linear polypeptides must end with a C-terminus.
This is the end of the section that is repeated for each atom for input_style 'polypeptide builder'
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Send comments to: Marcus G. Martin

Last updated: December 22, 2006