It's an explicit solvent simulation and I do have an ATOMIC_NUMBER section
in my prmtop. LEaP gave my dummy atoms a -1 value for atomic number in
the prmtop so I guess that's why pmemd got concerned. I suppose I can bow
to the tyranny of the periodic table and pretend like I'm using a real atom
....
--Niel
On Thu, Oct 24, 2013 at 1:14 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Oct 24, 2013 at 3:53 PM, Niel Henriksen <shireham.gmail.com>
> wrote:
>
> > Hi all,
> >
> > pmemd from a recent GIT pull crashes if I'm using a dummy atom whose mass
> > and atom name do not fall within categories in the get_atomic_number
> > routine in pmemd_lib.F90.
> >
> > Is there any reason not to just print a warning? It's easy enough for me
> > to change my atom mass/name to work, but I want to make sure I'm not
> > missing something here ....
> >
>
> Are you running a GB calculation? Does your topology file have an
> ATOMIC_NUMBER section? The get_atomic_number should only be called when
> the atomic number is not available in the topology file.
>
> You could always use ParmEd to add the atomic number section if it's not
> present (it will just pick the element whose mass is closest, regardless of
> atom name).
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Thu Oct 24 2013 - 14:00:02 PDT
