-
Hello.
This is awesome work.
I have also been working on this. I have run some tests with the espaloma approach using the method described here. [https://github.com/choderalab/espaloma/issues/192]…
-
Looks like something is wrong with the definition of `parameterize_small_molecule` - molflow raises an exception while loading it. Unfortunately this causes `molflow info` to fail.
This is **not a …
-
The stuff in pyopenmm is pretty questionable. We should move the needed features to a separate repo and provide some sort of testing / quality control / docs.
-
Related to #247 - currently Yank has systembuilder, which probably ought to be split off into a more general-purpose tool that will be useful aside from just for Yank workflows (i.e. setup of GROMACS …
-
For reasons that make the implementation in the toolkit tractable, the toolkit groups multiple virtual particles into virtual sites so that a _virtual site_ can, and often does, define a group of sev…
-
We need to settle how to handle non-ThermoML datasets within the `PropertyCalculator` framework, most immediately for calculation of equilibrium expectation values of other properties.
As noted here …
-
-
Hello everyone,
is it possible to change the atomic charges on the fly (or is there an easy way to do it)?
-
This thread breaks out the discussion from #31 into a separate thread about how we should handle residue replacement.
I would like to propose we work toward having pdbfixer use three possible modes f…
-
(Continuing from #206)
**Describe the problem**
Problem 1:
Our current data structures and functions handle aromaticity in an unsafe way. There are three places where we store aromaticity infor…