pdbfixer
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openmm
[FR] Support for modeling non-standard residues
I don't know if this should be formally included in PDBFixer, but it might be nice to implement a plugin library (kinda like what wetmsm is to msmb) that allows PDBfixer to model non-standard residues.
I know for my own work, I've been interested in simulating acetylated/methylated residues and have had to rely on Rosetta for my pipeline. Rosetta works fine internally, but makes the code difficult to share and almost impossible to test on travis.
Also, how difficult might this be to implement? It seems like most of the work would come from curating more templates for PDBFixer to read.
See also #44 and #31.
#44 has some useful concrete proposals.
Do you need to just model in these residues, or do you need to simulate then in OpenMM afterwards too?
Ah #44 seems ideal!
And yes, I would want to simulate the resulting structures in OpenMM. Hopefully, the pipeline would look similar to what we've already set up with ParmEd and PyRosetta.
Any progress on this (or #31/#44)? Would be great to have this working, as PyRosetta has become all but unusable at the moment.
I haven't worked on either of those. If this is important for you, we can try to push up the priority of them.
I think these would be great. Happy to contribute to their implementation, but we should be sure to define what the modes will do in a way we can all be happy with.
I still like the #44 proposals. What do you guys think?
If this is important for you, we can try to push up the priority of them.
Yes. This and de novo sequence generation (e.g. creating short linear peptides) would be very helpful.
Yes. This and de novo sequence generation (e.g. creating short linear peptides) would be very helpful.
Agreed, though you can easily do this right now with LEaP (which is installable via conda with ambermini).
Agreed, though you can easily do this right now with LEaP (which is installable via conda with ambermini).
Oh good point! Then #44 should have higher priority.