Aha! I should have chosen "AMBER Coordinates with Periodic Box" manually.
VMD automatically chose just "AMBER Coordinates" (for implicit solvent, as
I understand it).
Everything looks good now.
Thanks,
Enrique Frio
On Tue, Mar 29, 2016 at 8:10 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> You'll need to tell us exactly what you did. For example, did you load the
> prmtop using the amber 7 topology, followed by the trajectory using amber 7
> coordinates with box? And is this the direct trajectory output from MD and
> the same prmtop as used for simulation, or has either been processed or
> changed?
> On Mar 29, 2016 8:05 AM, "Enrique Frio" <enrique.frio.gmail.com> wrote:
>
> > Hello all,
> >
> > An MD simulation in Amber14 looks weird in VMD 1.9.2 but looks perfectly
> > fine in Chimera.
> >
> > There seems to be a "tail" and some protruding parts that appear to
> trace a
> > path below (and sometimes in other places elsewhere) the protein being
> > simulated (this is part of the equilibriation stage). Please see attached
> > photo.
> >
> > Any ideas/ advice? Thanks!
> >
> > --
> > Cheers,
> > Enrique
> > <http://www.rbc.org/odb/odb.shtml>
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
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>
--
Cheers,
Enrique
<http://www.rbc.org/odb/odb.shtml>
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Received on Tue Mar 29 2016 - 06:00:03 PDT
