-
There seems to be a mismatch between the definition of the equilibrium torsion angle in openmm for periodic torsions, and MDTraj compute_dihedrals function.
OpenMM periodic torsion defines 0 degree…
-
**Reported by akdehof on 26 Jan 38814018 14:13 UTC**
There is preliminary student-code, that creates an arrow and a widget to simplify the manipulation of torsion angles. The task is to tidy-up and ba…
-
If possible, add the code used to generate `glycan_torsion_angles` to https://github.com/arviz-devs/arviz_example_data. @agustinaarroyuelo
-
Hi,
I am interested in using [MP-Nerf](https://github.com/EleutherAI/mp_nerf) for a custom dataset and in order to do this I would need to have the functionality of transforming arbitrary PDB entr…
-
I love the feature for constrained geometry searches that allows you to point and click at the bonds, angles, torsions to be constrained.
It would be amazing if there was a similar feature for poi…
-
To do :
Move methods for setting torsion angles and bond angles from CG_folding to CG_movers
Need these to be generalizable based on ID of monomer
`set_bb_angles(pose, dict)`
where `dict` i…
-
In alchemical free energy calculations, we often need to define torsions and angles in a way that may introduce numerical instabilities (eg. morphing into nitriles, ring opening/closing, etc.). Typica…
-
Part of charge development for carbohydrate molecular dynamics simulations requires an ensemble charge set. This charge set is built from PDB files which were extracted at regular intervals from a pr…
-
Now,I have dihedral angle data for a protein. Can litemol visualize it?
-
The original AlphaFold paper describes the second stage of 3D structure prediction as using Gradient Descent to converge on a structure based on distance and angle samples taken from the output of the…