[AMBER] single strand RNA parameters

From: Jorge Iulek <jiulek.gmail.com>
Date: Wed, 10 Feb 2021 15:41:56 -0200

Dear all,

     Just to be sure, is there a way to use cpptraj to calculate single
strand (ss) RNA structure parameters with its nastruct tool?  As far as
I understand, it works only for double strand (ds) nucleic acids, right?

     I see that individual torsional angles and ring puckering's can be
calculated otherwise, but there are some other parameters that would be
useful for me, like twist, roll, tilt, etc. By the way, this is a ssRNA
with a number of methylations; residue mapping seems to have worked fine.

     For while, the way out of this I see is to generate pdb coordinates
of each frame of the trajectory and to use a 3rd part program to do
that, one example might be x3dna.

     But I wonder of other (maybe easier/more direct way) suggestions.



AMBER mailing list
Received on Wed Feb 10 2021 - 11:00:02 PST
Custom Search