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, as 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.
That problem is remedied by adding 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 other force fields.
Improper torsions
The 'mgmstereo' improper torsion is 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.
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.
List the actual atom number instead of the names, but this example shows the general concept.
- 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
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