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
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Received on Thu Feb 11 2021 - 10:00:02 PST
