Ah okay. Sorry then. But if its only the atom names that dont match, isn't it worth a try to either name them correctly in the pdb file(maybe via a little script) or to adjust the names in the topology file so they match the pdb? (I know, very simple-hearted question.)
________________________________ Von: [email protected] im Auftrag von albert Gesendet: Mo 30.05.2011 09:37 An: Discussion list for GROMACS users Betreff: Re:AW: Re: [gmx-users] where can I download POPC membrane file? 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" <[email protected]> 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: [email protected] 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" <[email protected]> wrote: You can build it using VMD (VIsual Molecular Dynamics) 2011/5/30 albert <[email protected]> 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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