Hello,
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).
Hope this helps,
Jason
On Wed, Aug 11, 2010 at 11:35 AM, Bala subramanian <
bala.biophysics.gmail.com> wrote:
> Friends,
> I have protein-rna complex. I opened xleap as follows
>
> $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
>
> Then i opened my pdb with loadpdb command. What i would like to know is
> that
> in this case, will xleap automatically assign ff99 params to rna and ff99SB
> to the protein. Or pricesely is this the correct way to use ff99SB + ff99
> combination for protein and RNA.
>
> Thanks,
> Bala
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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 Aug 11 2010 - 09:30:03 PDT
