Hi Justin, Thanks for your email. I have modified it and the topology looks fine to me or at least I can't see any problem with it but still genion does not like it? Would please have a look? https://drive.google.com/file/d/0B0YMTXH1gmQsSl9KbWhXaWJKc1k/view?usp=sharing https://drive.google.com/file/d/0B0YMTXH1gmQsMjlMTlNPeWJqdkk/view?usp=sharing
Thanks James On Fri, May 15, 2015 at 4:36 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/14/15 1:25 AM, James Lord wrote: > >> Hi all, >> I am trying to neutralize this system (1HFX.gro) and genion is complaining >> about solvent not being continuous,then I made the 1HFX_modified.gro in >> which >> I have replaced HOH from 1HFX.gro with SOL and cut paste them at the end >> of >> the file. I am expecting gromacs to do the reordering for SOL. Am I >> missing >> anything? >> > > The topology needs to be modified in a similar manner. IIRC it is > topological continuity that genion checks. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.