Sir,
When I did the simulations with:
tleap -s -f leaprc.ff99bsc0
loadoff RNA_CI.lib
source leaprc.gaff
...
I did not notice any perturbation in the RNA structure. So is it necessary
to repeat the calculations using ff14SB?
On Fri, Oct 24, 2014 at 2:45 AM, Jiri Sponer <sponer.ncbr.muni.cz> wrote:
> I have now noticed several papers telling
> that either DNA or RNA has been simulated
> with ff99SB, Hornak et al 2006. Basically,
> it is impossible to tell which DNA or RNA force
> field has been used, as no nucleic acid force field
> is mentioned. Jiri
>
>
>
>
> On Thu, 23 Oct 2014, pavel.banas.upol.cz wrote:
>
> Date: Thu, 23 Oct 2014 22:54:28 +0200 (CEST)
>> From: pavel.banas.upol.cz
>> Reply-To: AMBER Mailing List <amber.ambermd.org>
>> To: AMBER Mailing List <amber.ambermd.org>
>> Subject: Re: [AMBER] Forcefield for RNA
>>
>>
>> Dear all,
>> the loading of force fields is indeed confusing when one is focused on
>> non-
>> protein systems. Contemporary generic force field is loaded by learrc.ff14
>> SB, which is however labeled according to its protein part. Thus many
>> users
>> are confused and usually believe that SB correction is crucial for nucleic
>> acids or at least it is worth to try. They do not even realize that is
>> absolutely irrelevant for nucleic acids, while they should pay attention
>> elsewhere.
>>
>> Possible solution would be to return back to the arrangement as it was for
>> ff10, where force field was loaded as f10 that contained SB for proteins,
>> bsc0 for DNA and bsc0+chiOL3 for RNA as a one simple but black-box
>> package.
>> Or alternatively split leaprc files to be system specific, so that user
>> will
>> have to choose proper force field variant for its particular system and in
>> case of hybrid systems such as protein+DNA complexes to explicitely ask
>> both
>> for protein and DNA force fields. However, then the leap should complain
>> when user will try to use e.g. protein force field for DNA.
>>
>> Pavel Banas
>>
>>
>> --
>> Pavel Banáš
>> pavel.banas.upol.cz
>> Department of Physical Chemistry,
>> Palacky University Olomouc
>> Czech Republic
>>
>>
>>
>> ---------- Původní zpráva ----------
>> Od: David A Case <case.biomaps.rutgers.edu>
>> Komu: AMBER Mailing List <amber.ambermd.org>
>> Datum: 23. 10. 2014 13:55:31
>> Předmět: Re: [AMBER] Forcefield for RNA
>>
>> "On Thu, Oct 23, 2014, Asfa Ali wrote:
>>
>>>
>>> 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?
>>>
>>
>> This is what you get by loading leaprc.ff14SB, as described in section
>> 3.2.2
>> of the Amber14 reference manual.
>>
>> Developers: this section far more confusing than it needs to be,
>> and detailed instructions for Amber are very sparse. You don't find out
>> until the final sentence what is in ff14SB for RNA, and I don't see any
>> place that documents what is going on for DNA. The promised leaprc file
>> for DNA has not yet been prepared. Table 3.1 marks ff99 as "current"
>> (!?!?). We need explicit instructions on which leaprc (or other) files
>> to load to get particular behavior. Basically, Section 3.2.2 has a good
>> general overview of nucleic acid force fields, but too little in the way
>> of specific information about Amber.
>>
>> ...dac
>>
>>
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>>
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>
--
Asfa Ali
Prof. S. Bhattacharya's group,
Dept. of Organic Chemistry,
Indian Institute of Science,
Bangalore-12
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Received on Fri Oct 24 2014 - 06:00:04 PDT
