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12.5.2 Chain Closure Degree of Freedom

The chain closure degree of freedom calls the modified Go and Scheraga chain closure procedure. This procedure find atomic positions for the backbone atoms starting with the residue given by the STARTRES option and continuing to residue STARTRES+2. In residue STARTRES, the position of the N must be known; in residue STARTRES+2, the position of CA, C, and O must be known. In addition, STARTRES cannot be the first residue in a protein chain, although STARTRES+2 can be the C terminal residue. This degree of freedom can handle all the natural amino acids as well as amino-isobutyric acid (AIB).

The MAXDT option specifies (in degrees) how much variation in peptide bond angles is permitted for a chain closure. The default value of 5 degrees should be adequate for most applications.

The MAXG option controls how bond angle adjustments are made. The default value gives good results. See the source code file, clschn.flx, for more details.

MAXEVDW specifies the largest energy permitted for a repulsive contact for any atom generated in the chain closure. Its value is specified in degrees.

CISTRANS controls whether the chain closure routine will generate cis prolines for any position within the three residues being constructed. ALLCISTRANS controls whether cis prolines can be generated for any residue, proline or otherwise.