Thanks Jiri.
I will consider your recommendations and I will have a look into the papers.
Yes, the script is already for H-bonds. Cpptraj is full of possibilities.
Yours,
J.
On 2/11/21 4:59 PM, Jiri Sponer wrote:
> 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 Sat Feb 13 2021 - 03:30:02 PST
