Thanks Jason and Daniel for the quick response!
Regards
Carlos
2015-05-07 13:17 GMT-03:00 Daniel Roe <daniel.r.roe.gmail.com>:
> On Thu, May 7, 2015 at 7:49 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
> >> how
> >> does cpptraj recognizes and corrects it afterwards ?
> >
> > I may be mistaken here, but I think cpptraj sees the "N" and figures
> > Nitrogen is the best match for the element.
>
> Cpptraj actually determine elements in two ways. First, if masses are
> available cpptraj will use the first letter of the atom name and the
> mass to determine the element. If this is unsuccessful, it will then
> try to determine the element from the whole atom name (this is where
> it catches weird names like IM for Cl- and IP for Na+).
>
> -Dan
>
> >
> >> I'm using Glycam_06j and AMBER 14, by the way.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Thu May 07 2015 - 10:00:04 PDT
