-
**Describe the bug**
When optimizing molecule conformers using UFF, sometimes the lowest energy conformer has 2 H atoms in (nearly) identical positions. The UFF energy for this conformer can be lower…
-
### Labels
[BUG][MAJOR]
### Description
title
### Steps to reproduce
1. blow up the boundary part of the mineral magnet
2. summon ore
3. no forcefield where you blew up the boundary
…
-
These ff libraries come from merging master (dna ff) and proline branches (protein ff), and then merging dna and protein forcefields so that they are in a single folder. It is likely the resulting lib…
-
Hi there!
First thank you for your great work here!
I'm a newcomer to openmm and currently try to set up an MD simulation of a protein with a small non-standard ligand using GAFF. To get starte…
-
I've been using light.exe's ability to recompute the lighting data for compiled BSPs to adjust old Quake 2 maps for use in the Remaster (as otherwise transparencies such as water surfaces and forcefie…
-
Spin out of a discovery in https://github.com/ParmEd/ParmEd/issues/486 that ffxml written using Types instead of Classes for PeriodicTorsionForce gives wrong energies.
Tracked this down to the lack …
-
- keep only final xyz
- parse out the other fields
- reparse
example scripts:
- loading the entire database
- Akshat will only need the dipole and polarizability only at the dft lev…
-
Hi,
I am wondering what would be a clean way to create a protein ligand system where the ligand is parametrized with
one of the MLFFs ?
In the example it is shown how to create a mixed syst…
-
- [ ] I believe this to be a bug with Open Babel
- [ x] This is a feature request
## Environment Information
Open Babel version: 3.0.0 from conda-forge, python 3.6
Operating system and versi…
-
I want to convert the N-Terminal Q residue into pyroglutamate (pE) in the structure of my protein and simulate it with Openmm. I will use charmm36 forcefield for this. But is non standard residual f…