cpptraj
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Amber-MD
Biomolecular simulation trajectory/data analysis.
1. By residue functionality. 2. Only specify part that needs to be remapped.
Dear Thom; Dear Dan, many sincere thanks for your prompt and truly helpful response! In fact, I wouldn't like to add solely 'dumping' functionality to CPPTRAJ, just to produce further...
- Enable 3d dataset OP scalar. - Identify voxels that correspond to ligand (with/without Gaussian, similar to volumetric mapping) for certain calculations. - Scripts from T. Balius, S. Ramsey &...
For atom types not currently handled by `surf`.
Otherwise in parallel each thread writes to the same file.
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...
Hi Dan, Sorry for getting back to you so late. Can you help to add a function into cpptraj to calculate the electric field of certain groups on a certain...
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).
@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...