I'm docking a small molecule into an enzyme utilizing using match style constraints and the EnzRepackMinimize Mover. The constraint is between my small molecule and a cofactor in the enzyme.
I've generated the params file for both my small molecule and the cofactor. When I run my script with the following distance constraint, everything works fine.
CONSTRAINT:: distanceAB: 1.2 0.1 1000 0 2
When I run my protocol trying to turn on the covalency term as in the following line
CONSTRAINT:: distanceAB: 1.2 0.1 1000 1 2
in my constraint file: to reduce repulsive effects, I receive the following error:
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AddOrRemoveMatchCsts - cstadd=======================
protocols.toolbox.match_enzdes_util.EnzConstraintIO: read enzyme constraints from 07a.cst ... done, 1 cst blocks were read.
protocols.toolbox.match_enzdes_util.EnzConstraintIO: Generating constraints for pose...
core.chemical.Patch: [ WARNING ] Patch MP-H7-connect implies it can apply to residue type AAA, but actually applying it fails.
core.chemical.Patch: [ WARNING ] You may want to check your patch definitions.
core.pose.util: [ ERROR ] Can't find residue type 'AAA:MP-H7-connect' in type set of mode fa_standard
Segmentation fault (core dumped)
I think this is, as it mentions, something to do with a patch file for my small molecule (assigned as AAA) but I can't seem to find too much information on generating a path file for small molecule specifically or, more generally, what patch handles the distance covalency term and what it can be applied to.
Thanks for the help!