Relax structure with metal cofactors

[Anonymous]

Hello,

I am trying to relax the pentameric 1SAC PDB file with its 10 calcium cofactors. I first removed other ligands from the file (ACY, acetic acid molecules) that I am not interested in, and left the calcium heteroatoms. I scored the PDB file using score_jd2.linuxgccrelease with the command lines flags -in:auto_setup_metals, -ignore_unrecognized_res, and -out:pdb. This worked well, and recognized the connectivity of the metal atoms with the appropriate residues. It also output a scorefile with a new scoring term called “metalbinding_contstraint” (scored using Talaris2014).

Then I tried went to relax the resulting PDB. I used the following command line flags:

…/relax.linuxgccrelease     -s 1SAC_mBIO.pdb     -relax:constrain_relax_to_start_coords     -relax:coord_constrain_sidechains     -no_optH false     -optH_MCA true     -flip_HNQ     -ex1     -ex2     -use_input-sc     -nstruct 10     -in:auto_setup_metals

In the tracer outpout, I can see that the metal/residue connections are again being recognized and that the “metalbinding_constraint weight was set to 1.0” for the Talaris2014 scoring. The relax then exits due to the following error:

AngleConstraint::score: warning: 0-length bonds!

[ERROR] EXCN_utility_exit has been thrown from: src/core/scoring/constraints/AngleConstaint.cc line: 231

ERROR: false

I read on the “Work with Metalloproteins” page (https://www.rosettacommons.org/docs/latest/rosetta_basics/non_protein_residues/Metals) that the flag -in:auto_setup_metals will auto create angle constraints for metal ions, and I should not have to specify the metal using the -extra_res flag and CA.param file since most metals are already in the fa_standard residue set.

It seems that I missing something. Any help would be appreciated!

Thanks,

Hannah

[Anonymous]

Follow up question: If I use the -auto_setup_metals flag during the structure scoring, do I also have to also use it for the subsequent relaxation? Or will there be information written into the PDB about the metal-residue connections already?

Thanks,

Hannah

[Anonymous]

Follow up question: If I use the -auto_setup_metals flag during the structure scoring, do I also have to also use it for the subsequent relaxation? Or will there be information written into the PDB about the metal-residue connections already?

Thanks,

Hannah

[Anonymous]

Follow up question: If I use the -auto_setup_metals flag during the structure scoring, do I also have to also use it for the subsequent relaxation? Or will there be information written into the PDB about the metal-residue connections already?

Thanks,

Hannah

[Anonymous]

This is a bug related to the combination of  -relax:constrain_relax_to_start_coord and  -in:auto_setup_metals that has been fixed with the Rosetta 3.8 release.

Also, the changes that the -auto_setup_metals flag invokes do not carry through in any output PDB, so you would have to include that flag during any subsequent steps.

[Anonymous]

This is a bug related to the combination of  -relax:constrain_relax_to_start_coord and  -in:auto_setup_metals that has been fixed with the Rosetta 3.8 release.

Also, the changes that the -auto_setup_metals flag invokes do not carry through in any output PDB, so you would have to include that flag during any subsequent steps.

[Anonymous]

This is a bug related to the combination of  -relax:constrain_relax_to_start_coord and  -in:auto_setup_metals that has been fixed with the Rosetta 3.8 release.

Also, the changes that the -auto_setup_metals flag invokes do not carry through in any output PDB, so you would have to include that flag during any subsequent steps.

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