[gmx-users] Secondary structure propensity.

[Sundari]

Thanks a lot ...

On Sun, Feb 18, 2018 at 9:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/18/18 6:05 AM, Sundari wrote:
>
>> Thank You :)
>>
>> I have a little doubt now. If I want total percentage of all 8 secondary
>> structures separately i.e SS (%) than I can get this by simply averaging
>> the propensities of ss ?
>>
>>
> No, that will give you a constant number. All residues have to be in one
> type of secondary structure (including coil) and they can only interconvert
> between them. If you do any sort of averaging over the 8 types, you get a
> constant. The calculation I gave before will do what you want.
>
> -Justin
>
>
>
>>
>> On Fri, Feb 16, 2018 at 6:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 2/16/18 3:40 AM, Subhomoi Borkotoky wrote:
>>>
>>> Hello,
>>>>
>>>> I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file ,
>>>> it
>>>> contains the required information.
>>>>
>>>> Only indirectly, but scount.xvg has all that is needed, the number of
>>> residues in a given secondary structure as a function of time. From that,
>>> percentage over time is a trivial scripting task, [(# in SS) / (# of
>>> residues)]*100.
>>>
>>> -Justin
>>>
>>> Regards,
>>>
>>>> S. Borkotoky
>>>>
>>>> On Fri, Feb 16, 2018 at 1:30 PM, Sundari <sundi6170 at gmail.com> wrote:
>>>>
>>>> Dear gromacs users,
>>>>
>>>>> can any one please tell me that how we get the secondary structure
>>>>> propensity or secondary structure content(%) as a function of
>>>>> simulation
>>>>> time.
>>>>>
>>>>> I used "gmx do_dssp" but it gives me number of residues forming the
>>>>> secondary structure vs simulation time. is it same thing or something
>>>>> different?
>>>>>
>>>>> Thank you in advance..
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>>>>>
>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
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>>>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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