Dear Shawn,
cpptraj from amber has a large number of parameters it can calculate,
with some specific routines to nucleic acids.
My hello to Rutgers, too!
Jorge
On 12/26/24 20:46, Shawn R wrote:
Dear Colleagues,
I am trying to characterize nucleic acid duplexes with parameters such as
minor/major groove widths, helix diameter and length, A and B form, etc. I am
wondering if there is software that does all of these things. I've used x3DNA
and DSSR, but they don't provide all of the descriptors I am looking for
(though they are both wonderful and have been very useful). Many publications
I've seen use CURVES+, but as far as I can tell, that server has not been
available in a number of years. Manually measuring all of these parameters
would take too much time over 10s of structures, unless such information is
described easily in ChimeraX/PyMol/Coot/MOE that I am not aware of.
Thanks for any insights!
Shawn
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