protons
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choderalab
OpenMM testbed for constant-pH methodologies.
Hi, I am not sure if this is the right place to ask for help. If not, sorry for this. Actually I want to titrate a few residues at the...
https://github.com/choderalab/protons/blob/master/examples/Ligand%20example/imidazole.xml#L24 @jchodera notes: For example, we have `` denote a residue, `` denotes an atom. The ` tag doesn't denote a proton, but a block of information defining parameters for...
 Breakdown of an Abl NCMC benchmark.
We currently don't have a way to handle syn- and anti- protons for carboxylic acids in ligands. The octa-acids may need to have this feature.
Now that we've settled on a datafile format, we should make a module that can plot the data we have. This should include ways to - [x] visualize a calibration...
Tweaks for calibration plots suggested by @jchodera * make sure the figure width is set to one column (3.5 inches?) * reduce the axis label font size * increase the...
We need to decide on the rest of the figures for the paper. For example, we will need to summarize results of constant-pH simulations of complexes and their impact on...
We want to pick a default - [ ] NCMC protocol ( could use linear for everything) - [ ] Desired simulation length - [ ] pH values of interest
Add new data and running scripts, and clean up files that used the old API in https://github.com/choderalab/constant-ph-systems repo, and start adding new systems to it.
We have settled and fixed most bugs in the netCDF4 format. We should automate the BAR analysis procedure.