[gmx-users] No default U-B types charmm

[gromacs query]

>> What atom numbers are on line 184419? What atom types are they in the
[atoms] section for that [moleculetype]?

These are waters only (I am using tipS3p CHARMM TIP3P). UB should not be
there. I am following Justin's suggestion to remove moleculetype from top
file (still not solved and trying, will let you know; I am newbie to
gromacs)

thanks


On Mon, Mar 3, 2014 at 6:48 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> On Mon, Mar 3, 2014 at 7:25 PM, gromacs query <gromacsquery at gmail.com
> >wrote:
>
> > Hi Justin
> >
> > Its problem with the waters I think.
>
>
> Can't be, they have no U-B.
>
>
> > I found conflict in water atom names:
> >
> > charmm36-jan2014.ff/tip3p.itp:
> > 1       OT      1       SOL              OW             1       -0.834
> > 2       HT      1       SOL             HW1             1        0.417
> > 3       HT      1       SOL             HW2             1        0.417
> >
> >
> >
> > charmm36-jan2014.ff/merged.itp
> > [ TIP3 ]
> >   [ atoms ]
> >       OH2    OT   -0.834  0
> >        H1    HT    0.417  1
> >        H2    HT    0.417  2
> >
> >
> > In PDB from charmgui its OH2,H1,H2. I changed names in
> > charmm36-jan2014.ff/tip3p.itp as in merged.rtp but still I get same
> error.
> >
> >
> >
> >
> > On Mon, Mar 3, 2014 at 5:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 3/3/14, 10:57 AM, gromacs query wrote:
> > >
> > >> Hi All
> > >>
> > >> I am trying to use charmm36 (charmm36-jan2014 from charmm website)
> with
> > >> popc membrane built using charmm-gui (have water and ions).
> > >>
> > >> I used commands as follows:
> > >>
> > >> pdb2gmx -f step5_assembly.pdb -o popc.gro -water tip3p -ff
> > >> charmm36-jan2014
> > >> editconf -f popc.gro -o popc_box.gro -c -d 0.0
> > >> grompp -f minim.mdp -c popc_box.gro -p topol.top -o em.tpr
> > >>
> > >> I get this error: (so many)
> > >> ERROR 11520 [file topol.top, line 184419]:
> > >>    No default U-B types
> >
>
> What atom numbers are on line 184419? What atom types are they in the
> [atoms] section for that [moleculetype]?
>
> Mark
>
>
> > >>
> > >> Where are UB for charmm36?
> > >>
> > >>
> > > This shouldn't happen.  Can you please identify what atoms are causing
> > the
> > > failure?  It may help to simplify by working only with a single lipid
> > > rather than a full membrane.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 601
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
> > > --
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