On Thu, 2014-01-23 at 18:19 +0530, esther nehu wrote:
> Dear Amber,
>
> I want to prepare an input file for a non-standard nucleic bases, how to
> prepare the pdb file and derive the charge parameters. Thank you.
Have you looked at the Amber tutorial pages?
http://ambermd.org/tutorials/
Look at the two Tutorial A1 (Advanced Tutorials) pages for details.
Of course you can also look at R.E.D. tools and their database to see if
they have already parametrized the non-standard bases you want. Their
webpage is
http://q4md-forcefieldtools.org/
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 23 2014 - 05:30:02 PST
