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 <[email protected]> wrote: > Hi Jack, > >> On Mon, Jan 4, 2010 at 2:44 AM, Tsjerk Wassenaar <[email protected]> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
