Thanks a lot ... On Sun, Feb 18, 2018 at 9:19 PM, Justin Lemkul <jalem...@vt.edu> 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 <jalem...@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 <sundi6...@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-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 >>> >>> * 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 > > * 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. > -- 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.