For nucleic acids:
ff10 = ff99 + bsc0 + reparameterized glycosidic torsions
The paper describing the glycosidic torsion reparametrization is here:
Performance of Molecular Mechanics Force Fields for RNA Simulations:
Stability of UUCG and GNRA Hairpins
Banas et al. J. Am. Chem. Soc. 2010 v6 pp 3836–3849
http://pubs.acs.org/doi/abs/10.1021/ct100481h
Unless you have a specific reason not to, you would want to use ff10
rather than ff99bsc0 to simulate a nucleic acid.
To answer the OP's other question, ff10 and ff99bsc0 are compatible with
AMBER9, no need to upgrade.
-Hugh Heldenbrand
Graduate Student, University of Minnesota
On 09/22/2011 08:50 AM, Brian Radak wrote:
> If I'm not mistaken (and someone please correct me if I am wrong), for
> nucleic acids ff10 is exactly equivalent to ff99 + the bsc0 parameters. Of
> course, ff10 also includes the non-trivial shift to new solvent models
> (TIP4P-Ew and the Joung/Cheatham alkali and halide ions).
>
> In short, I believe the conventional wisdom now is to always use ff10
> whenever possible. I don't know of any reasons why you wouldn't be able to
> do this with any recent release of AMBER (9, 10, 11, etc)
>
> Brian
>
> On Thu, Sep 22, 2011 at 9:41 AM, souvik sur<souviksur.hotmail.com> wrote:
>
>>
>> Hello,
>>
>>
>> Can the ff99 force field is comparable with parm bsc0 ?
>>
>> Is it possible to run
>> parm bsc0 in amber9 ? or higher version of amber is required for that?
>>
>>
>>
>> regards,
>> Souvik Sur
>> Ph. D. Student
>> Department Of Chemistry
>> University Of Delhi
>> India
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Thu Sep 22 2011 - 08:30:03 PDT
