And how ILDN modifications? Are they anywhere in Amber11?
Thanks,
Alan
On 11 August 2010 17:12, case <case.biomaps.rutgers.edu> wrote:
> On Wed, Aug 11, 2010, Jason Swails wrote:
> >
> > ff99SB is the ff99 force field that fixes a couple torsion parameters (4
> of
> > them total). All other parameters are those of ff99. If you want to
> > simulate Nucleic acids, you should probably load leaprc.ff99bsc0 instead
> of
> > leaprc.ff99SB. This will load ff99SB parameters to be used for proteins
> > along with parmbsc0 for nucleic acids (which is updated from ff99).
>
> Just an update/clarification: for historical reasons, ff99bsc0 only
> applies the "Barcelona modifications" to DNA, not to RNA. If you want
> RNA to have those modifications (and you will have to read the literature
> carefully to decide this), use leaprc.ff10 (which is not well documented,
> but with uses ff99SB for proteins, and ff99bsc0 for both DNA and RNA.)
>
> ....dac
>
>
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--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Thu Aug 12 2010 - 03:30:03 PDT
