Ivy Zhang

Sorry about that! I forgot to copy and paste the updated SEQRES to `5udc_splitchain`. This is another issue we've been running into -- when pdbfixer faces a file that doesn't...

I tested #198 on 5udc.pdb, and am still seeing missing residues being built in mangled ways. See `test_198.py` in the attached files. Additionally, I think it would be very helpful...

The molecule is so mangled that OpenEye has trouble perceiving stereochemistry. Here is the output I get for check_stereo.py: ```Warning: OE3DToAtomStereo is unable to perceive atom stereo from a flat...

Note that Iván generated htfs using the vanilla `HybridTopologyFactory` for CCC->CCCC and the energy validation test yields the following results: with dispersion correction off: ``` zero state error: 1.96084504011651e-05, one...

We discussed this at the perses dev sync 9/6/22 and we decided that we should keep this issue open to address this discrepancy in the future.

> @zhang-ivy : Were these files used? If so, should we merge this PR, or close it? I'm not sure -- I prepped these for @rafwiewiora to put on fah,...

Outline for directory structure: - `coronavirus` - `system_preparation` - `literature` - README will contain table of each paper along with a short (2 sentence ish) summary - sub-directories for each...

Iván notes that this is not super high priority since we are in the midst of overhauling the API anyway

We can write a test that checks that the rest lambda values are changing (and between 0 and 1) when we use T_max != 300 K. We can do this...

It definitely supports ion-bound systems, my RBD:ACE2 systems have Zn ions bound. It should also handle GTP, though I've never tried it myself. I would just supply the apo and...