The code has been merged. Hopefully you will find it useful.
-Dan
On Thu, Feb 11, 2021 at 1:08 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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
> > >>>
> > >>>
> > >>>
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 11 2021 - 13:00:02 PST
