[gmx-users] Fatal error: Unknown bond_atomtype cn9 in Charmm27

[Mark Abraham]

... 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 <jalemkul at 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
> >
> > jalemkul at 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
>
> jalemkul at 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-request at gromacs.org.
>