Re: [AMBER-Developers] valid atomic name/mass required?

From: Jason Swails <>
Date: Thu, 24 Oct 2013 16:14:12 -0400

On Thu, Oct 24, 2013 at 3:53 PM, Niel Henriksen <> 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
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Thu Oct 24 2013 - 13:30:02 PDT
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