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Block (BLK) residues with undefined topology and parameters

The second relatively easy way of dealing with missing entries in the residue topology and/or parameters libraries is to use a ``block'' residue. These residues are restrained more or less as rigid bodies to the conformation of the equivalent residue(s) in the template(s). No chemical information is used. The template residues can themselves be defined as block residues. The symbol for the block residues is `BLK' in the four- and three-letter codes and `.' in the single-letter code. The atoms in a BLK residue include all uniquely named atoms from the equivalent residues in all the templates. The atom type of all BLK atoms is the CHARMM type `undf'. The IUPAC atom names (as opposed to the atom types) are the same as in the templates. The `undf' atom type for all BLK atoms facilitates using the PICK_ATOMS command for generating restraints on the `BLK' residues.

The `undf' atoms are treated differently from the other atoms during preparation of dynamic restraints: No pairs of intra-BLK atoms are put on the dynamic non-bonded list. Only the ``inter-BLK'' atom pairs and ``BLK-other'' atom pairs are considered for the dynamic non-bonded restraints. The radius of all block atoms is obtained from the $RADII_LIB library using the block atom names (as written out to a PDB file), not the `undf' atom type. All intra-BLK and inter-residue BLK restraints other than the non-bonded restraints have to be derived separately and explicitly by MAKE_RESTRAINTS command using RESTRAINT_TYPE = 'distance'. See script scripts/__homcsr.top for the routine that makes block restraints for comparative modeling by the `model' script. Lennard-Jones, electrostatic, and general non-bonded spline terms involving `undf' atoms are ignored by MODELLER.

For an example of how to use block residues, see the FAQ Section 1.9, Question 16.


next up previous contents index
Next: READ_RESTYP_LIB read Up: Modeling residues with non-existing Previous: Residues with defined topology,   Contents   Index
Bozidar BJ Jerkovic 2001-12-21