OK, you mean probably that differences between RNA and DNA in
"reparameterized glycosidic torsions".
If I understood well for both (RNA,DNA) is possible to use ff10 but only
in case
of RNA, "reparameterized glycosidic torsions" are used.
My previous question was more "user based" taking care here just
what is the best option to load in tleap when creating systems a), b), c).
Best wishes,
Marek
Dne Thu, 22 Sep 2011 18:15:28 +0200 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> 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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Received on Thu Sep 22 2011 - 09:30:05 PDT
