Re: [gmx-users] Secondary structure propensity.

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

Re: [gmx-users] Secondary structure propensity.

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

Re: [gmx-users] Secondary structure propensity.

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

Re: [gmx-users] Secondary structure propensity.

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

Re: [gmx-users] Secondary structure propensity.

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

Re: [gmx-users] Secondary structure propensity.

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