Re: [AMBER] single strand RNA parameters

From: Jorge Iulek <>
Date: Thu, 11 Feb 2021 14:41:54 -0200

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.



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:
> 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 <>
>> Reply-To: AMBER Mailing List <>
>> To: AMBER Mailing List <>
>> 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 <> 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
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Received on Thu Feb 11 2021 - 10:00:02 PST
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