Remodel’s problem in treatment with non-protein residues

[Anonymous]

Dear Rosetta folk,

I have a question regarding the treatment with non-protein residues, namely metal ion and DNA, on Remodel application. Since I had known about the Remodel feature to switch entire structure into centroid representation, which erases entire metal-binding geometry and confuses the Remodel a lot (from Rosetta forum post https://www.rosettacommons.org/node/9438), I implemented the RemoveMetalConnections mover in order to avoid any errors at the remodel stage (with intention to restore it after remodel stage).

Despite all efforts, which have been done, when I try to run Remodel for Zinc-containing protein, I got such an error:

File: src/core/chemical/ResidueTypeSet.cc:983

[ ERROR ] UtilityExitException

ERROR: Unable to find desired variant residue ‘ZN’. Attempted to add target variant(s) to ResidueType using both ResidueType base name ‘ZN’ and base ResidueType. Was attempting to add new variant type ‘LOWER_TERMINUS_VARIANT’

I have already taken a look over Rosetta databases for residue datasets. The parametric files for Zinc atom are present both for full-atom and centroid modes. I wonder, why Remodel is not able to recognise the Zinc atom. Would anyone here be kind to specify the reason of such Remodel behaviour and suggest any solution to tackle this problem, please?

In addition, I have another remark.

As it is claimed here https://new.rosettacommons.org/docs/latest/application_documentation/design/Remodel, that “In a starting PDB that has multiple chains, Remodel works on the first chain”. Nevertheless, I got such an error “ERROR: Assertion `!( has_lower_terminus && has_upper_terminus )` failed”, a typical error for multi-chain structure modelling on Remodel. So, why is Remodel still complaining about it, if it is instructed to work with only the first chain?

Could anyone specify, when “This section will change in near future”, please?

I attach the PDB, flag and XML files to this post.

I will be highly appreciated for your response, and I am looking forward to it.

Respectfully,

Corvin.

[Author]

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