Daniel R. Roe

Similar to the recently added `guessbp` option (#507) but give users a bit more flexibility. Something like: ``` nastruct basepair :995-1141 :1142-1288 ``` The `basepair` arg could be specified multiple...

http://glycam.org/docs/othertoolsservice/download-docs/publication-materials/md2noe/

E.g. if user reads in dihedral data and wants to generate a dihedral covariance matrix (recently mentioned on Amber mailing list by Thomas Fox).

Make 'makestructure' a Command Instead of an Action

8

@swails and @hainm, I'd like your feedback on this in particular since we've discussed things like this in the past (e.g. #179). Since they are really designed to operate on...

Store average coords/masses etc. Probably NetCDF.

Originally suggested by Xiang-Jun Lu: http://x3dna.bio.columbia.edu/docs/dssr-manual.pdf http://nar.oxfordjournals.org/content/early/2015/07/15/nar.gkv716.full.pdf

See #1083.

Right now `multidihedral` requires all 4 atoms be bonded. Should there be a keyword (or on by default) that all atoms do not need to be bonded?

modXNA is a method for generating non-standard amino acid residues. It would be nice if `prepareforleap` could interface with this in some way. https://modxna.chpc.utah.edu/

Create a conda package

18

This would make it easier for cpptraj to be part of Amber Classic