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