Justin, hello! In the algorthm presented in the tutorial there is one inconvenience that is many iterations of the shrinking/minimization of the protein ( e.g if i'd like to obrain good value for S per lipid for my structure). Is there any way to make this process automated ? ( e.g some program wich could do all of those operations untill defined value for some magnitudes would be reached )
Also I'd like to ask about g_membed. As I've understood for that program I need in merged pdb struture ( consist of my peptide inserted in the membrane ) as well as merged topology. Is there any way to prepare this data exept the way presented in your tutorial ? ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html) E.g I've heard that this could also be done via PyMol. Where I could find example of such preparation ? Thanks for your help, James 2011/10/15 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> Dear Gromacs's users! >> >> >> I'd like to simulate some membrane proteins in their native environment. >> >> Recently I've found a good tutotial of the same simulation of the KALP >> peptide in DPPC membrane (http://www.bevanlab.biochem.** >> vt.edu/Pages/Personal/justin/**gmx-tutorials/membrane_** >> protein/index.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html> >> ). >> >> Is there someone who have also tried to make thit tutorial ? >> > > Yes, per our server logs, several hundred people have :) > > > First of all its very intresting for me the positioning of the protein in >> the membrane via specific perl script called infrategro. What values for >> the cutoff radius as well as measurements of the area per lipid are most >> adequate for different membrane proteins? >> >> > The ones given in the tutorial work quite well. They are the defaults > suggested by the developers of InflateGRO. > > > Could you also tell me some alternative ways of full algorithm of the >> protein insertion in the membrane? >> >> >> > Careful use of genbox (but will require significantly more equilibration as > there will be large gaps), or g_membed. > > -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 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> >
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