maybe I should go directly from pdb2gmx to grompp seeing as I have already solvated and ionized the protein in VMD.
On Mon, Jan 4, 2010 at 8:04 PM, Jack Shultz <j...@drugdiscoveryathome.com> wrote: > I did a little more checking on the structures, I notice the results > from genion move part of the protein far outside the solvent box. I > shall try this without the genion step > I put all the files in the working directory for this preperation in a > zip archive under > > http://boinc.drugdiscoveryathome.com/1YQW.zip > > On Mon, Jan 4, 2010 at 2:22 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >> Hi Jack, >> >>> On Mon, Jan 4, 2010 at 2:44 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >>>> Hi Jack, >>>> >> >> <snip> >> >>>> After preparation with (V|NA)MD, did pdb2gmx correctly assign chains, >>>> or did it tie chains together? In the latter case it would have issued >>>> a number of "Long Bond Warnings". Did anything else odd show up in >>>> the output of any of those steps? Did you actually read through it? >> >> Post pdb2gmx/grompp output to help us help you. >> >> Cheers, >> >> Tsjerk >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> Computational Chemist >> Medicinal Chemist >> Neuropharmacologist >> -- >> gmx-users mailing list gmx-us...@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 >> > > > > -- > Jack > > http://drugdiscoveryathome.com > http://hydrogenathome.org > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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
