Hi, if you don't want to be very accurate, you can select basing on the residue name since LEU, ILE, VAL...etc, are universally considered hydrophobic
2012/11/14 Justin Lemkul <jalem...@vt.edu> > > > On 11/14/12 2:27 AM, Raj wrote: > >> Hi all, >> >> can some one tel me how can i prepare a index file specifying the >> hydrophobic atoms along for measuring the hydrophobic contacts in the >> systems alone. >> >> > There is no straightforward way to do this, as far as I know. I generally > construct such groups by selecting groups of hydrophobic residues and then > parse out the hydrophobic atoms within these groups. You can narrow down > your selections using default groups like Sidechain (since the protein > backbone is highly polar) and select by atom type using a .tpr file as the > input to make_ndx. > > -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> > -- Cordiali saluti, Dr.Oteri Francesco -- 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