PATCH_SS_MODEL -- guess MODEL disulfides from model structure

TOPOLOGY_MODEL = $\langle{\tt integer:1}\rangle$

3

selects topology library: 1-9

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.