Oops, there's an .rtp entry. Shame on me :$ Maybe a good idea though to post the output of pdb2gmx.
Cheers, Tsjerk On Tue, Nov 17, 2009 at 3:44 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Justin, > >> What is the problem? It looks like you got everything to work, but the .pdb >> file you've posted is misformatted on the CL lines: >> >> ATOM 14 C14 PCD 1 -2.372 -1.395 0.000 1.00 0.00 >> C >> ATOM 15 CL1 PCD 1 5.070 1.618 -0.001 1.00 0.00 >> CL >> >> Note how the atom name "CL1" is shifted relative to "C14" so pdb2gmx handled >> it incorrectly. Formatting is not merely a suggestion! > > This is correct formatting, according to the PDB file format! Of the > four character positions denoting the atom name, the first two are > used to indicate the element. > > But what is this talking about pdb2gmx if there's a hand written > .top/.itp file in stead of an .rtp entry? Of course it will fail. And > if that's not the problem, Nilesh is still not providing a proper > description of what he's doing. > > Tsjerk > > -- > Tsjerk A. Wassenaar, Ph.D. > > Computational Chemist > Medicinal Chemist > Neuropharmacologist > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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/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/mailing_lists/users.php