[gmx-users] Secondary structure propensity.

[Justin Lemkul]

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..
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/
>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

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

==================================================