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

[Mark Abraham]

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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