[gmx-users] Secondary structure propensity.

[Sundari]

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 ?




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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>>
>>
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