There's a quick & dirty workaround. You can write a script to "g_sas" each frame individually, writing many output files. Then grab the results from there.
Sent from my iPhone On Jul 7, 2011, at 9:17 PM, "Justin A. Lemkul" <[email protected]> wrote: > > > ahmet yıldırım wrote: >> There are hydrophilic and hydrophobic SASA values versus simulation time in >> the output file (area.xvg). I want to hydrophilic and hydrophobic SASA >> values versus residue. > > That's not implemented, but it would probably be rather easy to modify the > code to do so. > > -Justin > >> 2011/7/7 Justin A. Lemkul <[email protected] <mailto:[email protected]>> >> ahmet yıldırım wrote: >> Dear users, >> I want to calculate hydrophilic and hyrophobic SASA value of >> each residue in protein. I used a command as the following: >> g_sas -f run.xtc -s run.tpr -or protein_protein.xvg >> Select a group for calculation of surface and a group for output >> select a group: 1 (protein) >> select a group: 2 (protein) >> But there is SASA value of each residue in the output file. How >> can I seperate the residues as a hydrophilic and hyrophobic SASA? >> This is already in the output file. Check the legends of area.xvg >> and you will see. >> -Justin >> -- ==============================__========== >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://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 [email protected] >> <mailto:[email protected]> >> 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 [email protected] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists >> <http://www.gromacs.org/Support/Mailing_Lists> >> -- >> Ahmet YILDIRIM > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
