next up previous contents index
Next: MUTATE_MODEL mutate Up: Stereochemical parameters and molecular Previous: PATCH_SS_TEMPLATES guess   Contents   Index

PATCH_SS_MODEL -- guess MODEL disulfides from model structure

TOPOLOGY_MODEL = <integer:1> 3 selects topology library: 1-10

Requirements:
model

Description:
This command defines and patches disulfide bonds in MODEL using MODEL's current structure. A disulfide bridge is declared between all pairs of Cys residues whose SG-SG distances are less than 2.5. The covalent connectivity is patched accordingly.

This command should be run after READ_MODEL and before optimization to ensure that the disulfides are fixed properly and that no SG-SG non-bonded interactions are applied.

TOPOLOGY_MODEL is needed to make sure the correct atomic radii are used in CYS-CYS patching.

Example: See PATCH_SS_TEMPLATES command.



Ben Webb 2004-10-04