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>
>
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>
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Received on Tue Mar 29 2016 - 05:30:06 PDT
