In addition to all the other responses, I just wanted to clear up why there is this difference in names. The POPC structure from the link below still has the atom names of the old CHARMM27 lipids (DPPC is fine). As suggested, a simple script can do the conversion for you.
Cheers Tom albert wrote: > I know this, but this file cannot be used because the atom name is quite > different from gromacs CHARMM36 topol library. > > > At 2011-05-30，"Rausch, Felix" <frau...@ipb-halle.de> wrote: > > Check this link given by another (unknown) mailing list user > yesterday (Topic name: *about POPC in Gromacs* )! > > http://terpconnect.umd.edu/~jbklauda/research/download.html > <http://terpconnect.umd.edu/%7Ejbklauda/research/download.html> > > ------------------------------------------------------------------------ > *Von:* gmx-users-boun...@gromacs.org > <mailto:gmx-users-boun...@gromacs.org> im Auftrag von albert > *Gesendet:* So 29.05.2011 21:23 > *An:* Discussion list for GROMACS users > *Betreff:* Re:Re: [gmx-users] where can I download POPC membrane file? > > But I don't think it is pre-equilibrium POPC membrane...... and more > over, the position from VMD is not pre-aligned with OPM database. It > would be a great problem for putting our protein in the membrane...... > > > > > At 2011-05-30，"Sergio Manzetti" <sergio.manze...@vestforsk.no > <mailto:sergio.manze...@vestforsk.no>> wrote: > > You can build it using VMD (VIsual Molecular Dynamics) > > > > 2011/5/30 albert <leu...@yeah.net <mailto:leu...@yeah.net>> > > Dear all: > > I would like to use charmm36 and POPC for membrane protein > simulation. and I am wondering where can I download charmm36 > pre-pribriumed POPC PDB and topol file for gromacs? > > Thank you very much > Best > > -- > gmx-users mailing list gmx-users@gromacs.org > <mailto: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 > <mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- Dr Thomas Piggot University of Southampton, UK. -- 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
