On Thu, Oct 24, 2013 at 4:47 PM, Niel Henriksen <shireham.gmail.com> wrote:
> 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
>
Then this should not be a problem. I'll look into it.
Thanks,
Jason
> ....
>
> --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
> >
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 24 2013 - 14:00:03 PDT
