-
While working on https://github.com/mosdef-hub/mbuild/pull/1191 in mBuild, I noticed that it should be relatively straight forward to move the [Charmm par writer ](https://github.com/mosdef-hub/mbuild…
-
Hello
I am a beginner and I have a question. Can I take these parameters for MD simulations with the CHARMM force field? If it's possible, what types of files do you recommend using??
-
It has been suggested that providing molecular movies from the CHARMM trajectories might be a nice feature to add to BilboMD
-
Dear all,
I've installed the tool (pypka) using pip3 install pypka inside a conda envs, during these step, I do not have any error, but when i running using : python3 -m pypka parm.dat, where "p…
-
Hi, OpenMM community.
I have prepared my system with CHARMM-GUI and generated the openmm input files. However, when I try to run the calculation with the executable README, I get this error:
```…
-
In line with the overall [API proposal](http://alchemlyb.readthedocs.io/en/latest/api_proposal.html), we want to have parsers for each of the major MD engines, and eventually have coverage for all of …
-
**Reported by oliver on 8 Nov 38772708 15:33 UTC**
There are improper torsions missing in CHARMM (EEF1 at least). This leads to skewed rings, e.g. in
Trp.
Check missing impropers (need to go back to …
-
Hi,
For a known complex 1Z92, i wanted to find the interactions usinng bindppi.
I took the pdb from RSCB PDB.
I am using the docker , so to run that i ran the command
`
docker run -v /home/u…
-
Would be cool to have a working version on the most recent CHARMM force-field
-
I wanted to point out a few things:
1. OpenMM has a python `Topology` object that looks fairly similar to your `Molecule` object, which might be helpful for interconversion
2. OpenMM has python-base…