cpptraj
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Amber-MD
Biomolecular simulation trajectory/data analysis.
When saving pdb file from LES parm7 and rst7: ``` bash ATOM 74 CG2 VAL 5 2.113 13.231 12.603 1.00 0.00 C ATOM 75 CG2 VAL 5 2.672 12.986 10.766...
as we discused on gmail, I prefer to have an option to keep the extension. `.rst7.1` --> `.1.rst7` `.pdb.1` --> `.1.pdb` Rationale: Many programs recognize files based on extension. So...
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
Hi sir, I would like to ask about creating mw covariance matrix. Do I need to align the frames before creating matrix? I am planning to compute configurational entropy for...
Feature request - Local Distance Difference Test (lDDT) analysis as described in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799472/
Hi, I would like to calculate with cpptraj an activation index which is based on a set of distances and coeffiecients My idea was the follwoing script ``` parm prod1/structure.psf...
