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Error Implementing Match Style Constraints

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Error Implementing Match Style Constraints


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!



Post Situation: 
Thu, 2019-12-19 09:53