Re: [gmx-users] Secondary structure propensity.

[Sundari]

Thanks a lot ...

On Sun, Feb 18, 2018 at 9:19 PM, Justin Lemkul  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  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  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/
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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
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>>
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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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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Re: [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  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  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
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==


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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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Secondary structure propensity.

[Subhomoi Borkotoky]

Thanks for the addition.

On 16 Feb 2018 6:22 pm, "Justin Lemkul"  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  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-requ...@gromacs.org.
>>>
>>>
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@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
>
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Re: [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  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  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-requ...@gromacs.org.
>>>
>>>
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@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
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Secondary structure propensity.

[Justin Lemkul]

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  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!

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send a mail to gmx-users-requ...@gromacs.org.






--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Secondary structure propensity.

[Subhomoi Borkotoky]

Hello,

I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file , it
contains the required information.

Regards,

S. Borkotoky

On Fri, Feb 16, 2018 at 1:30 PM, Sundari  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-requ...@gromacs.org.
>



-- 
Yours Sincerely,
--
*Dr. Subhomoi Borkotoky, Ph. D.*
DBT Research Associate,
Kusuma School of Biological Sciences,
Indian Institute of Technology Delhi,
New Delhi-110016,
India.


https://scholar.google.co.in/citations?user=bJz7GokJ=en
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[gmx-users] Secondary structure propensity.

[Sundari]

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

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