Hello Hugh,
just to be sure:
ff10 = ff99 + bsc0 + reparameterized glycosidic torsions ?
or
ff10 = ff99SB + bsc0 + reparameterized glycosidic torsions ?
Thanks in advance !
Best wishes,
Marek
Dne Thu, 22 Sep 2011 17:02:40 +0200 Hugh Heldenbrand <helde010.umn.edu>
napsal/-a:
> 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 - 08:30:04 PDT
