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11.2 Holding Dihedrals Near Selected Values

Using this form of the CONS command, one may put constraints on the dihedral angles formed by sets of any four atoms. The constraints may be set to either a single angle, or to be bounded by two angles (a flat bottom well). The improper torsion potential is used to maintain said angles.

The command for setting the dihedral constraints is as follows:

11.3 Syntax of Dihedral Constraints

     CONStraint { DIHEdral [BYNUM] dihe-spec FORCE real MINimum real MAXimum real }
                { CLDH                                                            }

Syntactic ordering: DIHEDRAL or CLDH must follow CONSTRAINT, and FORCE and MIN must follow DIHEDRAL.

If BYNUM is specified, then

     dihe-spec ::= integer integer integer integer

If BYNUM is not specified, then

     dihe-spec ::= atom-spec : atom-spec : atom-spec : atom-spec :


     atom-spec ::= segid resid iupac

Note that colons must be used as delimiters following each atom-spec.

11.3.1 Function of Dihedral Angle Constraints

DIHEDRAL adds a torsion angle to the list of constrained angles using the specified atoms, force constant, and minimum and maximum dihedral angles. CLDH clears the list of constrained dihedrals so that different angles or new constraint parameters can be specified.

When a range of angles is specified, it is important to keep in mind that torsion angles are periodic. Therefore, the MINIMUM and MAXIMUM bounds are taken literally. Reversing the order of values specified for these variables has the effect of complementing the range of the angular constraints. For example, a specification of MINIMUM 175 MAXIMUM -175 is just 10 degrees, whereas the specification of MINIMUM -175 MAXIMUM 175 is 350 degrees.

In order to simplify the specification of constraints, there are a number of defaulting rules used by this command. First, for each atom which follows the first, you can omit segid's, resid's, and iupac names if they match values from the previous atom. Be careful here if any of the identifiers are also used for higher order structures. For example, if a protein has a segid of 1 and a resid of 1, then specifying a single 1 will be interpreted as a segment identifier. In all cases, use the PRINT CONS command to check that you got what you expected.

Next, omitted FORCE values will be taken from the previous constraint if it exists. MINIMUM and MAXIMUM values will also default to previous values if neither option is specified. However, if either one is specified, but the other is missing, then they default to each other, so that the effect is to use a single point harmonic well.

Do not use a value of -9999 as the minimum or maximum dihedral angle, since the program uses this value to indicate that no angle was found on the command line.

These constraints can be coupled to a conformational search. See the option, EPCONS, in Miscellaneous Global Options.

11.3.2 Other Commands

The PRINT CONS command, see Print Command, will work for constraints. As of now (October 13, 1992), one cannot analyze the contributions of this term using the analysis facility nor can one read or write the description of this term out. Someday ...