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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--
-------------------------
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Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
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Received on Thu May 07 2015 - 09:30:09 PDT
