Dear Justin, can you suggest me published paper related to about hydrophobic and hydrophilic contacts?
03 Temmuz 2011 00:24 tarihinde Justin A. Lemkul <[email protected]> yazdı: > > > ahmet yıldırım wrote: > >> Dear Justin, >> >> You said before "you can obtain some idea by using g_mindist to calculate >> hydrophobic and hydrophilic contacts between the protein and ligand". >> >> That is, I can explore whether there is hydrophobic or hydrophilic feature >> of ligand using g_mindist tool. is this correct? >> I did the calculations related to protein_ligand interactions (protein >> contains two ligand). I plotted the graphs of distance and numcount versus >> simulation time for each ligand. The number of contacts in ligand x is more >> than the other ligand y. Which of this ligands are hydrophobic? Which is >> hydrophilic? I know you are not private tutor. Please don't be angry :( >> >> > I certainly hope I haven't given the impression that I'm some angry tyrant. > I'm happy to answer reasonable questions across the list, time permitting. > > To obtain information about hydrophobic and hydrophilic contacts, you need > to use special index groups that tell g_mindist (or any other tool) which > atoms to consider. In this way, you can count how many of each type of > contact evolve over time. > > -Justin > > -- > ==============================**========== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [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]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM
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