2011/9/22 Marek Maly <marek.maly.ujep.cz>
> OK,
>
> perfect that.s what I wanted to know.
>
> So just to be really sure:
>
> In case of simulation:
>
> a)
> Nucleic acids systems: BEFORE bsc0 NOW equivalent with using ff10
>
Not quite. This is what Tom said:
>> > For nucleic acids:
>>
>> ...to clarify: for RNA:
>>
>> > ff10 = ff99 + bsc0 + reparameterized glycosidic torsions
>>
>> ...for DNA,
>>
>> ff10 = ff99 + bsc0
>>
>> (since the reparameterized glycosidic torsions do not work particularly
>> well for DNA).
>
> b)
> Proteins systems: BEFORE ff99SB NOW equivalent with using ff10
>
> c)
> Proteins + nucleid acids systems: BEFORE (ff99SB + bsc0) now equivalent
> with using just ff10
>
>
> Am I right ?
>
> Best wishes,
>
> Marek
>
>
>
> Dne Thu, 22 Sep 2011 17:24:56 +0200 Brian Radak <radak004.umn.edu>
> napsal/-a:
>
> > I believe ff99SB is only for amino acids (improves helicity or
> > something).
> > It is almost certainly included in ff10 by default.
> >
> > On Thu, Sep 22, 2011 at 11:15 AM, Thomas Cheatham <tec3.utah.edu> wrote:
> >
> >>
> >> > For nucleic acids:
> >>
> >> ...to clarify: for RNA:
> >>
> >> > ff10 = ff99 + bsc0 + reparameterized glycosidic torsions
> >>
> >> ...for DNA,
> >>
> >> ff10 = ff99 + bsc0
> >>
> >> (since the reparameterized glycosidic torsions do not work particularly
> >> well for DNA).
> >>
> >> --tec3
> >>
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> >
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>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Thu Sep 22 2011 - 09:30:04 PDT
