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 - 07:00:02 PST
