metals not being recognized in rosettaCM

[rlwoltz]

Hi all,

   I'm having an issue with my K+ and CA+ ions not being recognized in rosettaCM. I've tried the spacing of the ions a few times and the K.param files are there. I have K+ and Ca2+ in the pdb and it fails at the K+ atoms so not sure if the Ca2+ will work as it takes 4 hours for the script to fail. I did see a few discussions about metals but I either didn't think they were relevant or the solution did not work for me as they don't seem to have the same point of failure as I do. 

I've attached my a zip file as this is what is accepted but please see the pdb, xml, options file and output (rosetta-v3.out) and crash log if this is helpful to give me advice.

metal-ion-failure-files.zip

Here is my error:

core.conformation.Conformation: Found disulfide between residues 1270 1308
core.conformation.Conformation: Found disulfide between residues 1797 1835
core.conformation.Residue: [ ERROR ] Cannot build coordinates for residue K at position 2109: missing too many atoms.
core.conformation.Residue: [ ERROR ] Missing atoms are: K V1 V2
protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing protocol:

File: src/core/conformation/Residue.cc:1376
[ ERROR ] UtilityExitException
ERROR: Unable to fill in missing atoms.

protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job S_0001
protocols.jd2.JobDistributor: [ WARNING ] S_0001 reported failure and will NOT retry
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 5305 seconds

I think I ran into this problem a few years ago last time I tried something similar and the solution was to get rid of the ions for the rosettaCM step and then align the structures and reintroduce the ions in the final relax step which is separate. But I'd like to avoid this as it is a LOT of work for this work around for how many states of the protein I need to model at this stage.

It seems the pdb requires 3 atoms to complete the residue that rosetta is look for with the V1 and V2 not being recognized? Is this correct? If so can someone give an example of how a K+ "residue" would look with those extra virtual atoms (V1/V2) and what coordinates should I give the virtual atoms or do the coordinates not matter?

I apologize if this is a double post and if someone can link another discussion that is relevant I'm happy to follow those steps.

Thanks for any help that can be given,

Ryan