Dear Jorge, it is difficult to advice as I do not know the system you
study. Essentially, for each protein-RNA system one needs to find
some appopriate descriptors respecting a given specific structure (we
have published number of protein-RNA MD simulation studies, so you can see
them). So it depends on the structure at the protein-RNA interface.
In most cases it is important to first monitor mainly the protein-RNA
interactions, H-bonds, stacks. Their monitoring also gives an idea
if the trajectory is healthy or corrupted. If there is protein-RNA
simulaion study that does not monitor the interface then I do not read
the work irrespective of what the authors write.
ssRNA is going to adapt to the protein.
Best wishes, Jiri
On Thu, 11 Feb 2021, Jorge Iulek wrote:
> Date: Thu, 11 Feb 2021 14:41:54 -0200
> From: Jorge Iulek <jiulek.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: amber.ambermd.org, daniel.r.roe.gmail.com,
> Jiri Sponer <sponer.ncbr.muni.cz>
> Subject: Re: [AMBER] single strand RNA parameters
>
> 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 - 10:30:03 PST
