Hi everyone, First of all thanks to both of you for your quick replies. Dear Tsjerk, I’ll be much appreciated if you could send me the *itp file of POPC. Thanks a lot, Carlos
-- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile Teléfono: 56-71-201 798, Fax: 56-71-201 561 Email: carlos.navarr...@gmail.com or cnava...@utalca.cl On Saturday, December 13, 2014 at 12:21 PM, Tsjerk Wassenaar wrote: > Hey, > > The all atom mapping of Martini to CHARMM36 is available in > backward/initram, so the conversion can be done directly. You only need to > have a CHARMM36 POPC itp file. I can provide one if needed. > > Cheers, > > Tsjerk > On Dec 13, 2014 3:38 PM, "Justin Lemkul" <jalem...@vt.edu > (mailto:jalem...@vt.edu)> wrote: > > > > > > > On 12/13/14 12:47 AM, Carlos Navarro Retamal wrote: > > > > > Dear gromacs users, > > > I just ran a CG simulation of a system consisting in a protein embedded > > > in a POPC membrane solvated in water. > > > After that i ran the script .initram to obtain an AA representation of my > > > system (gromos54a7), but sadly i couldn’t find a *.itp with the > > > description > > > of the hydrogen atoms of the membrane. > > > > > > > > > Gromos96 54A7 is not all-atom, hence why the hydrogens are "missing." > > > > So, is there a way to add the missing atoms after this step? and if its > > > not posible, could someone provide me with the ‘correct’ *itp file > > > (hopefully gromos or charmm ff) ? > > > > > > > > > We include POPC in our CHARMM36 port, but you'll need to add an .hdb entry > > for POPC, which is largely very repetitive but very easy. > > > > http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs > > > > -Justin > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > > Department of Pharmaceutical Sciences > > School of Pharmacy > > Health Sciences Facility II, Room 629 > > University of Maryland, Baltimore > > 20 Penn St. > > Baltimore, MD 21201 > > > > jalem...@outerbanks.umaryland.edu > > (mailto:jalem...@outerbanks.umaryland.edu) | (410) 706-7441 > > http://mackerell.umaryland.edu/~jalemkul > > > > ================================================== > > -- > > 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 > > (mailto: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 (mailto: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.