Thank you justin
With best wishes and regards, Rama David On Fri, Nov 23, 2012 at 12:45 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/22/12 1:54 PM, rama david wrote: > >> Hi justin, >> Thank you for reply. >> As per your suggestion, >> The whole protein should always be the group for the >> surface calculation. Whatever subset of those atoms (i.e. residues of >> interest) can be the output group. >> >> So as per your suggestion I have to select the protein as my option 1 and >> for output I have to select the hydrophilic residues or hydrophobic >> residues as per my choice ....Is these is right ??? or Am I wrong??? >> ( That means I have to make to index file that contain two groups >> hydrophilic and hydrophobic residues.) >> >> Would you please tell me why not select the protein as output, as I am >> calculating the change in the hydrophilic and hydrophobic surface area of >> protein...??? >> >> > You can certainly do that. Perhaps I misunderstood the original post. I > thought you were curious about the solvent exposure of certain residues. > If you only care about the evolution of total polar and nonpolar surface > areas, then choose Protein for both groups. > > -Justin > > As per the manual, >> >> The program will ask for a group for the surface calculation and a >> group for the output. The >> calculation group should always consists of all the non-solvent atoms in >> the >> system. The output group can be the whole or part of the calculation >> group. >> >> >> >> As two protein comes closer in simulation they formed the antiparrallel >> beta strand, I want to find the change in hydrophilic and hydrophobic >> surface area of protein... >> >> >> >> With Best Wishes and Regards, >> Rama david >> >> On Thu, Nov 22, 2012 at 11:32 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 11/22/12 2:36 AM, rama david wrote: >>> >>> Dear user , >>>> I simulate the two protein in random coil position, when they come >>>> close >>>> they form antiparallel beta sheet structure. >>>> I want to calculate the change in hydrophilic and hydrophobic >>>> surface >>>> area over my simulation time. >>>> For usig g_sas Should I have to make the different index group for >>>> hydrophilic and hydrophobic residues >>>> Or should only have to select the option protein both the time. >>>> >>>> >>>> The whole protein should always be the group for the surface >>> calculation. >>> Whatever subset of those atoms (i.e. residues of interest) can be the >>> output group. >>> >>> -Justin >>> >>> -- >>> ==============================****========== >>> >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==============================****========== >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>> posting! >>> >>> * Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? 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