I meant subset :) On Wed, Dec 12, 2012 at 8:21 PM, Kavyashree M <hmkv...@gmail.com> wrote:
> Sir, > > Oh! I was using sunset index numbers for both. I am sorry. I will try > that and see. First option as protein and next the subset. Thank you > very much. > > Kavya > > > > On Wed, Dec 12, 2012 at 8:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 12/12/12 9:37 AM, Kavyashree M wrote: >> >>> Thank you very much for your replies. >>> >>> The system consists of a homodimer in tip4p dodecahedron box >>> simulated using OPLSAA ff. >>> >>> The A B C here are the amino acids: >>> A- S T N Q G P H >>> B- A V L I M C F Y W >>> C- D E K R >>> >>> So these are set in an index file and i used each one of these >>> to calculate sasa in g_sas. >>> When the g_sas calculation starts it specifies the number of >>> hydrophobic atoms, one of the example - >>> For the whole protein - >>> 4644 out of 7590 atoms were classified as hydrophobic >>> For group A of same protein - >>> 702 out of 1424 atoms were classified as hydrophobic >>> For group B of same protein - >>> 2614 out of 3496 atoms were classified as hydrophobic >>> For group C of same protein - >>> 1328 out of 2670 atoms were classified as hydrophobic >>> >>> In this the number of hydrophobic atoms of A, B and C adds >>> up to the total hydrophobic atoms in whole protein. >>> >>> but after the calculation is over the average values of "Total" sas >>> (legend S2 of area.xvg file) of the protein and "Total" sas of A, B >>> and C are given below >>> Whole protein - 254.04nm^(-2) >>> A - 175.87nm^(-2) >>> B - 211.33nm^(-2) >>> C - 264.65nm^(-2) >>> >>> I expected that the average total sas of Whole protein atleast >>> approximately >>> equal the sum of Total sas of A, B and C. If not why? All calculations >>> are >>> done for the same trajectory after equilibrating. >>> >>> >> Are you selecting the correct groups when running g_sas? For instance, >> you should be selecting "Protein" for the surface calculation, and then >> your custom subsets for output. If you use the subsets for both surface >> calculation and output, you will get an artificially inflated value that >> includes extra surface area that is actually buried in the context of the >> whole structure. >> >> -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://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? Read >> http://www.gromacs.org/**Support/Mailing_Lists<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