Nathan Baker

@danny305 - we're more-or-less moved into the cloud now. Can you please provide a minimal example of the functionality you're hoping for with mmCIF?

Yes, that works. Thanks for the update.

Hi Danny - This isn't an immediate priority and we'd appreciate any help you can provide. We think we have protein mmCIF *parsing *working in the code now but would...

Hi James -- This is great! @intendo -- could you or Mark work with this? Thanks! On Fri, May 8, 2020 at 7:46 PM James Loy wrote: > Hi @sobolevnrm...

Yes, thank you.

Oops... @speleo3 just told me I totally misunderstood this issue and the original intent was to have PDB2PQR produce mmCIF that APBS and other programs could consume.

I believe this is where the molecule is chosen for the coordinates: https://github.com/Electrostatics/apbs/blob/c2e5af22c9044b2bb8f9c1114710add58ec5b007/src/mg/vpmg.c#L958

Thank you very much!

Running `pdb2pqr 1tiv.pdb 1tiv.pqr --ffout=CHARMM --titration-state-method=propka --with-ph=2` generates protonated versions of ASP and GLU with inconsistent residue names for atoms within a single residue. For example: ``` ATOM 20 N...

PDB2PQR appears to be treating these changes like CHARMM patches (e.g., see https://github.com/openmm/openmmforcefields/issues/22) rather than renaming full residues. This is done in various places in the code by an `if`...