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MCCCS Towhee (MGM Steroechemistry Enforcer)

 

 

Overview
    This section covers the MGM Stereochemistry Enforcer improper torsion as implemented into the towhee_ff_mgmstereo file in the ForceFields directory. This is by no means a complete force field, it only exists to enforce L or D (or if you prefer R or S) stereochemistry. This is needed because configurational-bias is easily able to switch stereochemistry of a center during a configuartional-bias regrowth. This is remedied by added this improper torsion onto the stereochemical center.

     

MGM Stereochemistry Enforcer in Towhee
    There are no atom names for this force field, it is used in combination with another force field.
Coulombic interactions
    There are no specific coulombic interactions for this force field as it is used with other force fields.
Improper torsions
    The 'mgmstereo' improper torsion can be combined with other forcefields by listing an improper torsion with a type of -1. This triggers a special flag in assemble.F to look for the mgmstereo improper torsion instead of searching the atom types of the actual force field for the molecule. In order to use this improper you need to define three improper torsions. If you wanted to define an "L" stereocenter on an amino acid Calpha you would define the following torsions from the Calpha atom. You would list the actual atom number instead of the names, but this gives the idea.
    N Halpha Cbeta -1
    N Cbeta C(=O) -1
    N C(=O) Halpha -1
    In order to define a "D" stereocenter you simply reverse the atom orders.
    N Cbeta Halpha -1
    N C(=O) Cbeta -1
    N Halpha C(=O) -1
Proteins
    This is often used with a protein force field. See the improper torsion section for more information.
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Send comments to: Marcus G. Martin
Last updated: September 07, 2005