[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 <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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Justin A. Lemkul, Ph.D.
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