Much appreciated, works beautifully!
On 10/10/07, TJ Piggot <[EMAIL PROTECTED]> wrote: > > Just as a note editconf will covert a pdb to a gro file > > Tom > > --On Wednesday, October 10, 2007 09:47:03 -0400 Adam Fraser > <[EMAIL PROTECTED]> wrote: > > > Yes I tried this and it doesn't work for me. I get: > > > > > > Fatal error: > > Library file ffG53a6.n2t not found in current dir nor in default > > directories. > > (You can set the directories to search with the GMXLIB path variable) > > > > Also, doesn't x2top take in a gro file? (not a pdb) I wrote a script > > that converts pdb to gro, and I still get the above error. > > > > -Adam > > > > > > On 10/10/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > > > > Adam Fraser wrote: > >> Hello, > >> > >> I'm very new to Gromacs, and I am interested in simulating the > >> interactions of 2 hexadecane (C16H34) molecules in water (SPC/E > >> specificall). I've spent some time experimenting with tutorials in > >> Gromacs, but I've found little help in non-protein simulations like > this > >> one. > >> > >> I've built topologies for hexadecane compatible with NAMD, so I figure > I > >> should be able to do the same in Gromacs but I'm fuzzy on how to go > >> about doing so (what files to edit). I was also hoping to get some > >> input on which forcefield would be best for this sort of system. > >> > >> I'd greatly appreciate it if someone could give me some pointers on how > >> to get started here. > >> > >> Thanks very much, > >> Adam > >> > > if you have a pdb file you can run x2top (3.3.2 only). > > > >> > >> > ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> gmx-users mailing list [email protected] > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > > > > -- > > David van der Spoel, Ph.D. > > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > > > > > > ---------------------- > TJ Piggot > [EMAIL PROTECTED] > University of Bristol, UK. > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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