Hi, Thanks dear Justin for useful reply,
I have a system that is contained of protein-water-ions. I want to calculate residue SAS of protein. In the first way, I select a group consisting protein for calculation, and then this protein for output. At the second way, I select the whole system first for calculation, and then protein for output. The SAS_calculations of residue protein are different in two ways. I have two questions. Q1- Why results are different in two ways? Q2-Can anyone demonstrates clearly how residue SAS of protein calculate in two ways? Q3- what property or quantity do I can get from The SAS_calculations of residue protein in two ways? Best wishes, Afsaneh On 3/15/12, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > afsaneh maleki wrote: >> Hello dear user, >> >> I have a system that is contained protein-water-ions. I used the >> following command: >> g_sas -f free.xtc -s free.tpr -o area -or res_area -oa >> atom_area –q -nopbc >> >> I select the whole protein first for calculation, and then this protein >> for output.In this way I can obtain Area per residue from "res_area" file >> and >> area per atom from "atom_area" file. >> >> How to get area per residue with data of area per atom from "atom_area" >> file? When I average on area per atoms for a selected residue, it >> doesn't correspond with area per residue for a selected residue from >> "res_area". > > It shouldn't. Averaging the areas per atom should not produce anything > related > to the constituent residue(s). The sum of the atom areas should yield the > residue area. A quick look through the code seems to indicate that this is > true, that is, the two quantities are not produced independently; residue > area > arises from atom area. > > -Justin > >> How to correlate area per residue for a selected residue with area per >> atoms for a selected residue? >> >> Thanks in advance, >> Afsaneh > > -- > ======================================== > > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
