Thank you so much for the above suggestions.
I have tried the following:
tleap -s -f leaprc.ff99bsc0
loadoff RNA_CI.lib
source leaprc.gaff
....
and carried out the initial file preparation. There was no error/problem as
the structures after simulation runs were looking fine. So is the above
fine?
Also, as advised by Jiri Sponer, I didn't try chiOL3 along with ff99bsc0.
If I have to do so, should I load both the force fields simultaneously?
On Thu, Oct 23, 2014 at 4:37 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, 2014-10-23 at 11:22 +0530, Asfa Ali wrote:
> > Hi all,
> >
> > I wanted to know whether the forcefield ff99bsc0 suitable for RNA
> > simulations? Or is ff99SB better?
>
> In addition to advice you have already received, I suggest you look at
> the third chapter of the AmberTools manual, which has a lengthy
> discussion on force field choices in Amber (along with a set of
> references for further study if needed).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Asfa Ali
Prof. S. Bhattacharya's group,
Dept. of Organic Chemistry,
Indian Institute of Science,
Bangalore-12
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Received on Thu Oct 23 2014 - 04:30:03 PDT
