Thanks, Daniel. I will check it out.
J.
On 2/11/21 6:38 PM, Daniel Roe wrote:
> The code has been merged. Hopefully you will find it useful.
>
> -Dan
>
> On Thu, Feb 11, 2021 at 1:08 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>> Hi,
>>
>> I have a pull request to implement this calculation via the 'sscalc'
>> keyword: https://github.com/Amber-MD/cpptraj/pull/881
>>
>> Once the pull request is merged in feel free to try it out. Should be
>> by the end of today.
>>
>> -Dan
>>
>> On Thu, Feb 11, 2021 at 12:41 PM Jorge Iulek <jiulek.gmail.com> wrote:
>>> 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 - 03:30:03 PST
