... and please suggest a correction to whoever distributed such a non-conforming parameter set.
Mark On Mon, Jan 16, 2017 at 7:45 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/16/17 4:02 AM, Mijiddorj Batsaikhan wrote: > > Dear Justin, > > > > Thank you very much for quick response. > > > > I want to capitalize cn9, but I could not find small cn9 in my force > field. > > There is CN9 (capital) only for DNA. There is not any DNA molecules in my > > system. > > > > The error you posted before comes from a bonded interaction using cn9. > This > means it's somewhere in ffnabonded.itp, probably in [dihedraltypes]. The > fact > that CN9 is used by DNA only does not depend on the contents of your > system; the > force field itself must be syntactically correct. > > -Justin > > > > > Best regards, > > Mijiddorj > > > > > > > > On 1/15/17 11:04 PM, Mijiddorj Batsaikhan wrote: > >> Dear gmx users, > >> > >> I am using gromacs-v5.1 with charmm27 force field that extended by > >> swissparams D amino acids. > >> > >> I got a following error. > >> > >> ************************************* > >> Fatal error: > >> Unknown bond_atomtype cn9 > >> ************************************* > >> I searched some solutions, but there is no clear solution. > >> I also checked in atomtype.atp, etc., I could not find cn9, There are > all > >> CN9. > >> > >> How can I fix this error? please advice me for modification of FF. > >> > > > > Capitalize it. GROMACS atom types are case-sensitive. > > > > -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 > > > > ================================================== > > > > -- > ================================================== > > 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.