For RNA, you need to have chiOL3, to prevent spurious ladder-like
structure. For RNA it is even more important than bsc0.
alpha/gamma bsc0 is intended to prevent loss of DNA structure.
chi chiOL3 is intended to prevent loss of RNA structure.
You really need to READ first, before simulating.
Jiri
On Thu, 23 Oct 2014, Asfa Ali wrote:
> Date: Thu, 23 Oct 2014 16:56:48 +0530
> From: Asfa Ali <asfa.iisc.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Forcefield for RNA
>
> Thank you so much for the above suggestions.
>
> I have tried the following:
> tleap -s -f leaprc.ff99bsc0
> loadoff RNA_CI.lib
> source leaprc.gaff
> ....
>
> and carried out the initial file preparation. There was no error/problem as
> the structures after simulation runs were looking fine. So is the above
> fine?
>
> Also, as advised by Jiri Sponer, I didn't try chiOL3 along with ff99bsc0.
> If I have to do so, should I load both the force fields simultaneously?
>
> On Thu, Oct 23, 2014 at 4:37 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Thu, 2014-10-23 at 11:22 +0530, Asfa Ali wrote:
>>> Hi all,
>>>
>>> I wanted to know whether the forcefield ff99bsc0 suitable for RNA
>>> simulations? Or is ff99SB better?
>>
>> In addition to advice you have already received, I suggest you look at
>> the third chapter of the AmberTools manual, which has a lengthy
>> discussion on force field choices in Amber (along with a set of
>> references for further study if needed).
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Asfa Ali
> Prof. S. Bhattacharya's group,
> Dept. of Organic Chemistry,
> Indian Institute of Science,
> Bangalore-12
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Oct 23 2014 - 14:00:03 PDT
