I was following an Amber8 tutorial. I have downloaded the nuc.in and on
running nucgen the following appears:
unknown flag: nuc.out
usage: nucgen [-O] -i ngin -o ngout -d ngdat -p pdbout.
I dont understand where ive gone wrong. Can you tell me how to proceed?
On Thu, Jan 23, 2014 at 6:38 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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 Sat Jan 25 2014 - 04:00:03 PST
