Dear Tsjerk I had a similar question. I guess insane.py script is supposed to build a coarse-grained membrane/solvent system from scratch. But, if I already have a particular existing atomistic configuration of lipid/water system along with some proteins ( which I had obtained by performing an atomistic simulation), how do I generate a coarse-grained martini counter-part of that specific atomistic snapshot ?
Your suggestion will be very helpful. jagannath On Sat, Feb 27, 2016 at 3:29 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Ali, > > The current version of martinize is for coarse graining proteins and > there's a version for nucleic acids. Lipids are not supported yet. These > you could forward map with the program backward, but why the hassle as you > can also directly build the coarse grain membrane/solvent system with > insane (http://www.cgmartini.nl/index.php/downloads/tools/239-insane). > > Hope it helps, > > Tsjerk > On Feb 26, 2016 22:36, <khourshaeisha...@mech.sharif.ir> wrote: > > > > Dear all > I want to simulate a system of 128 DPPC with 3655 water molecule which its > .pdb file is available on professor tielman website. I want to Coarse > grain it but apparently at first i should turn the pdb file into > appropriate type for using with martini. I understood, I should use marti > ize.py to convert the pdb but I dont know how. Also the tutorial wasnt > helpful. Could anyone give me the direct command to do this ? > best regards > Ali > ================== > Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir) > Department of Mechanical Engineering > Sharif University of Technology, Tehran, Iran > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.