thanks for the note. Yes I meant a single chain name. The minimization for those few bonds should not be too arduous. Hope it works out. Paul
> On Oct 10, 2018, at 1:22 PM, Kit Sang Chu <ks...@ucdavis.edu> wrote: > > Hi Paul, > > Giving the same name you mean same "chain name"? I tried but the problem > persists. For my specific case I cannot add extra amino acids. I just have > to minimize the energy to pull them closer. > > Regards, > Simon Kit Sang Chu > Ph.D. student > Biophysics Graduate Group > University of California Davis > > > On Wed, Oct 10, 2018 at 3:48 AM paul buscemi <pbusc...@q.com> wrote: > >> Try giving residues in the macro-macro structure the same name … or >> possibly get rid of the 10A gap by using additional amino acids like >> gly-gly gly ? >> >> >>> On Oct 9, 2018, at 5:28 PM, Kit Sang Chu <ks...@ucdavis.edu> wrote: >>> >>> Hi everyone, >>> >>> I have a macromolecular structure which contains multiple copies of >>> proteins. Initially, there are separate monomers and now I have to join >>> some of them through N/C-terminals. >>> >>> However, editconf fails to recognize the merging part, possibly because >>> they are separated by ~ 10A. All monomers supposed to be merged are given >>> the same chain name in pdb. All hydrogen and terminal oxygens are >> stripped >>> out. >>> >>> Are there any criteria specifically for GROMACS to recognize for merging? >>> Is there any specification / flag to force merging terminals? >>> >>> Thanks, >>> Simon >>> -- >>> 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. > -- > 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.
