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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…
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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??
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Hi,
I wanted to add a phosphorylation patch to my peptide, but I haven't been able to do it successfully using HTMD.
I was wondering which is the correct way to add a phosphoserine patch. I have a…
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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…
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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 …
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**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 …
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Would be cool to have a working version on the most recent CHARMM force-field
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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…
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I am trying to get the pka for 1tiv.pdb and write the output using the CHARMM naming scheme. It appears that the residues names are inconsistently named. Namely, pdb2pqr 1tiv.pdb 1tiv.pqr --ffout=CHAR…
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Currently, there is no possibility to read in CHARMM velocity files. These are binaries, very similar to CHARMM dcds, just with a slightly different header, and the data block contains velocities sav…