Hannah Baumann

Should have \sum_n W_nk = 1 error with pymbar3.0.5 while analysis is working with pymbar3.0.3

30

Hi, I'm analyzing free energy calculations (Gromacs-based) using alchemlyb. The analysis fails due to following error: Warning: Should have \sum_n W_nk = 1. Actual column sum for state 0 was...

Filter that disallows hybridization changes

1

In some mappings in ligands in the PLB system, mapping atoms that are connected by single or double bonds can lead to problems. It would be great to see if...

Changes PLB from openfe

11

As discussed with @ijpulidos and @jchodera , here the PR from the changes that we made to the PLB. See below for a list of things that have been changed...

Error when trying to assign partial charges to the eg5 cofactor using openff-toolkit/openeye am1bccelf10

1

I'm getting this error when assigning partial charges using openeye's am1bccelf1 via the openff-toolkit: ``` def gen_charges(smc): offmol = smc.to_openff() offmol.assign_partial_charges('am1bccelf10') print(offmol.partial_charges) return openfe.SmallMoleculeComponent.from_openff(offmol) ``` `cofactor = gen_charges(c)` ``` ValueError:...

Questions regarding specific ligands in the PLB

4

I have some questions that came up when going through the PLB: 1. in some datasets, some of the ligands are deposited more than ones, but they have the same...

Ring substituents for some ligands in different orientations, even though same substituent

1

I noticed that for some ligands (in the SHP2 and CDK8 sets), ring substituents point into different directions which can potentially lead to sampling problems in the RBFE calculations (if...

Add a warning/note in the setup that protein inputs may need to be equilibrated before running RBFE?

1

Simulations can crash (give NaN errors) if the protein has not been equilibrated first. Maybe we could add a warning or note in the documentation that proteins may need to...

Assuming they provide extra benefits (Mobley lab to investigate), we should benchmark running a mix network combining RBFEs and SepTop.