Amos Anderson

A user of my tool reported this problem to me, too, in his case from Arginine, which I haven't bothered trying to resolve with PDBFixer.

In my case, I think I'm using post-7.2.2, although I haven't updated since July I think. According to `conda list`, I'm using openmm 7.3.2 py36_0 omnia/label/dev However, if I dig...

I did just get an OPM aligned 4yay and a memembed aligned 3o7qA to work with POPC. Maybe POPC is more likely to work than POPE?

I've switched to the dev version of openmm (7.3.2) and I'm seeing the same issue. Here's a script: ``` fixer = PDBFixer(filename="4yay.pdb") fixer.findMissingResidues() fixer.findNonstandardResidues() fixer.replaceNonstandardResidues() fixer.findMissingAtoms() fixer.addMissingAtoms() fixer.addMissingHydrogens(7.0) print('\nAdding membrane:',args.membrane_lipid_type)...

I've been working away at this. I've integrated Rosetta relax into my project and can use it to refine the structure before trying to add the membrane. I've attached the...

I would definitely not want it to change the protonation state of residues that already have hydrogens, but I didn't investigate if that's happening or not. Maybe that's implied by...

I wrote some sample code like this: ``` pp = pprint.PrettyPrinter(indent=3,width=200,compact=False) def displayStatistics(fixer,summary): summary["chains"] = [] for c in fixer.topology.chains(): numResidues = len(list(c.residues())) numAtoms = len(list(c.atoms())) composition = defaultdict(int) for...

Residues which were initially assigned to be HIE or HID are becoming HIP.

Ah, OpenMM's behavior for automatically selected variants is intentional then -- not a bug. Sorry, I could have found and read that doc myself. 😊 To get the behavior I...

Ok, here's a code snippet. I believe this should be included in `OpenMM` because a) to my knowledge there's no accepted standard for the names of these variants, b) these...