-
Hello. The normal rdkit MolTransforms setDihedralRad function doesn't work at all for ring torsions. How can I manipulate the 3D geometry of a molecule with rings such as cyclohexanes?
Thank you
-
When training, the ligand's conformation is replaced by the one obtained by UFF and optimized according to the ground truth. However, in the evaluation in evaluate.py, you still use the virtual confor…
-
I'm currently attempting to convert parameters generated with CGenFF into a gromacs usable form, but am running into some issues. CGenFF returns a .str and .mol2 file rather than a .psf and .crd. Both…
-
@jchodera and I found in issue with the geometry proposals in WT RBD:ACE2 N501Y and beta variant RBD:ACE2 Y501N -- the CA chirality is R, not S. This happens in both apo and complex.
Note that for th…
-
I just wanted to make a brief proposal for a chemical environment sampling API.
The `ChemicalEnvironment` API (along with subclasses `AtomEnvironment`, `BondEnvironment`, `AngleEnvironment`, and `Tor…
-
When using a 10 or 20fs timestep, in the course of a simulation there will be energy spikes, up to the order of 1E12 kJ/mol. This is more prevalent for higher epsilon value (~2kJ/mol and higher) and a…
-
__ISSUE__
we have the ability to scan improper/ring-torsions now, but should we automatically apply some default limit on the scan range? or will torsiondrive cope with standard settings and stop gri…
-
# Aim
Define the structure of the database that IDPConformerGenerator needs to read and mine in order to build the conformers.
This database represents the file or structure that stores the whol…
-
United-atom types are quite popular in "data driven" force fields. For hydrocarbons the "virtual site" is located on the carbon atoms while the hydrogens are not accounted for explicitly. Hydrogens …
-
I am trying to run DiffDock on a batch of pdbs with the same ligand. For some of the pdbs I get this error, which results in no output for the given pdb.
However, this error seems to be random and …