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I run this code for proteins solvated in hexane. But some of my structures look like this and are just dispersed in space. no bonds.
my code:
```
from openmm.app import *
from openmm import *
…
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**Description**
Hello. I'm using bespoke to parametrize ligands for relative free energy calculations. I successfully parametrized tens of ligands. I'm currently struggling to efficiently integrate…
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**Describe the bug**
Previously, we had run into issues where the `openforcefield` toolkit using the OpenEye toolkit backend perceives trivalent nitrogens as stereocenters, causing issues for loading…
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I have a quick question about how atomic radii work. I have a situation where I need to pack to a relatively large density. I don't mind if some atoms overlap but it is critical that others don't. It …
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I'm not finding ~~triple bond parameters ... am I doing something wrong in my setup here?~~ yes I was, misreading the SMIRKS completely!
I'm using [this](https://raw.githubusercontent.com/jthorton/…
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**Description**
Please describe what you are trying to do, what you have done so far, and what you could use help with.
I am attempting to use bespokefit to parametrize the torsions for a molecu…
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Hello,
I'm trying to surround a receptor with solvent mix of ligand + water in 10:1 ratio (no ligand in binding site). When I open the resulting pdb with saved CONECT records in VMD and ChimeraX, I…
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I am testing psiresp to perform RESP calculation on a molecule with autogenerated conformatons, on a local qcfractal server. If I disable the conformer generation and do single conformation calculatio…
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**Describe the bug**
_originally posted by Bill Swope_
> Alberto and I have been looking at dipole moments for our neutral benchmark molecules and have discovered several issues that we feel shoul…
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Seem…