Hi,
I have a pull request to implement this calculation via the 'sscalc'
keyword: https://github.com/Amber-MD/cpptraj/pull/881
Once the pull request is merged in feel free to try it out. Should be
by the end of today.
-Dan
On Thu, Feb 11, 2021 at 12:41 PM Jorge Iulek <jiulek.gmail.com> wrote:
>
> Dear Daniel and Jiri,
>
>
> Thank you for your input.
>
> I should add that this ssRNA is bound to a protein, initially
> "ordered", and, to the study I am performing, it would be useful to
> check how long the bases keep "ordered", well "stacked". I thought these
> parameters might help on monitoring how the system evolves, though other
> parameters might also make some indication. Anyhow, as I mentioned,
> there is a way out that implies coordinate generation and the usage of
> an outside program, so I am going for it, despite the work involved with
> 200,000 coordinate sets (for while!). I do not know how usual studies on
> ss_NA's are common, such that the effort to enable nastruct to act upon
> them is worth, nevertheless.
>
> Yours,
>
>
> Jorge
>
>
> On 2/11/21 1:39 PM, Jiri Sponer wrote:
> > Dear all, I agree with Dan, these parameters are intended for duplexes,
> > they do not provide good description for ssRNA conformational space. Jiri
> >
> > -------------------------------------------------------
> > Jiri Sponer
> > Institute of Biophysics of the Czech Academy of Sciences
> > Kralovopolska 135
> > CZ-61265 Brno
> > Czech Republic
> > e-mail: sponer.ncbr.muni.cz
> > http://www.ibp.cz/
> > https://www.ibp.cz/en/research/departments/structure-and-dynamics-of-nucleic-aci
> > ds/info-about-the-department
> > -----------------------------------------------------------
> >
> >
> >
> > On Thu, 11 Feb 2021, Daniel Roe wrote:
> >
> >> Date: Thu, 11 Feb 2021 09:28:49 -0500
> >> From: Daniel Roe <daniel.r.roe.gmail.com>
> >> Reply-To: AMBER Mailing List <amber.ambermd.org>
> >> To: AMBER Mailing List <amber.ambermd.org>
> >> Subject: Re: [AMBER] single strand RNA parameters
> >>
> >> Hi,
> >>
> >> You're correct, currently the 'nastruct' code is only set up for base
> >> paired calculations. However, it would be relatively simple to apply
> >> the existing calculations (for tilt, shift, etc) to the reference axes
> >> for bases in a single strand. However, I'm not sure whether the
> >> information you get out of it will be useful - someone more
> >> knowledgeable about RNA structure may want to chime in. I'll play
> >> around with the code if I get the time and at least give users the
> >> option.
> >>
> >> -Dan
> >>
> >> On Wed, Feb 10, 2021 at 1:41 PM Jorge Iulek <jiulek.gmail.com> wrote:
> >>> 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.
> >>>
> >>> Yours,
> >>>
> >>>
> >>> Jorge
> >>>
> >>>
> >>>
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Received on Thu Feb 11 2021 - 10:30:02 PST
