Lee-Ping Wang
Lee-Ping Wang
I think the charge on this protein is -15, but PDBFixer only adds 9 positive ions. https://www.dropbox.com/s/r6sv73mglmu966f/3chy_native.pdb I replaced the nonstandard amino acid with CYS, deleted all heterogens and used...
As a force field developer and quantum chemistry user, I often find myself working with collections of structures (conformations) and associated energies. This could be useful for torsion drives in...
### Pandas version checks - [X] I have checked that this issue has not already been reported. - [X] I have confirmed this bug exists on the [latest version](https://pandas.pydata.org/docs/whatsnew/index.html) of...
* EITHER putting the OE license back, OR changing the little remaining functionality that requires it over to SDF (should be possible now that OFFTK supports partial-charges-in-SDF). I'd think that...
FB targets usually creates the Engine object by passing a dictionary that merges the target options and engine options dictionaries. There is the potential for namespace conflicts, in particular the...
To improve usability, the TorsionProfile target should be able to take user-supplied indices for the torsion atom indices rather than requiring metadata.json from QCArchive. I'll do this at some point.
Currently, FB includes kinetic energy terms in the gas and liquid phases when computing the heat of vaporization. I am pretty sure these terms are supposed to analytically cancel out...
Right now, parameter names like VDWS and VDWT (these are usually sigma and epsilon) are shared in AMBER .frcmod and GMX .itp formats. These parameters also have hard-coded rescaling factors...
Lately I've noticed an stochastic failure of one of my unit tests. I think this is due to the TINKER version update and their geometry optimization code being changed, but...
Progress and notes: - Parser for new data format **(100% done)** - Multiple files will be read into a single `DataFrame`. - The "system index" specifies an experimental data set...