As Professor Case mentioned, you also need some type of library file. For
example, an amber prep file, a mol2 file, or an amber OFF library file.
An frcmod file only contains force field parameters -- it has no information
regarding the residue's connectivity, structure, or anything else. This is
all detailed fairly extensively in the leap section of the AmberTools
manual.
Outside of these bits of advice, nothing more can be offered without a more
detailed breakdown of the exact commands, files, etc. that you used as well
as the exact errors that you received. Due to the complexity and
flexibility inherent in Amber programs (which helps make it more widely
applicable), a simple "doesn't work" is not useful in attempts to debug/fix
issues.
All the best,
Jason
On Wed, Feb 2, 2011 at 10:02 AM, subrata paul <paul.subrata34.gmail.com>wrote:
> Thank you sir
>
> I changed 0 to O but it's not work.
> what is wrong with this file?
> any other procedure for creating this molecule?
> I am using amber 10.
>
> thanking you
> subrata
> >
> >
> >
>
>
>
>
>
>
> > AMBER mailing list
> > > AMBER.ambermd.org
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> > --
> > Dr. Adrian E. Roitberg
> > Associate Professor
> > Quantum Theory Project, Department of Chemistry
> > University of Florida
> >
> > Senior Editor. Journal of Physical Chemistry.
> >
> > on Sabbatical in Barcelona until August 2011.
> > Email roitberg.ufl.edu
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Feb 02 2011 - 07:30:09 PST
