Yes, it may easily happen. Note that the beta parametrization
(bOL1) and thus OL15 complete version was published in autumn 2015.
So, in some papers less complete
versions could have be used, especially if you take into consideration
that the projects start 2-4 years BEFORE publication.
In addition, in principle, the OL dihedral potentials are modular,
so in principle you could use just some of them.
You probably refer to the
https://doi.org/10.1093/nar/gkx004,
where we indeed used Cornell+ff99+bsc0+ezOL1 for the DNA part,
exactly as specified in the work (and standard chiOL3 for RNA).
The paper was formally accepted in January 2017, but
it has been before several times rejected in other journals,
and even the NAR took extended revision (data received refers to
the re-submitted version). So in reality all our HIV-1 RT simulations were
done before OL15 has been available. ChiOL4 moduli was
not necessarily needed since in DNA/RNA hybrid the strands are more
or less canonical. So it is indeed pre-OL15 work.
Now we completely switched to OL15 in all DNA projects.
Best wishes, Jiri
On Thu, 17 Sep 2020, Jenny 148 wrote:
> Date: Thu, 17 Sep 2020 14:23:11 +0530
> From: Jenny 148 <jenny.rs140.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>, sponer.ncbr.muni.cz
> Subject: Re: [AMBER] Query on nucleic acid force fields
>
> Sir,
>
> I have been referring some papers and in one of your papers you have
> mentioned the use of ff99bsc0εζ OL1 forcefield( Rna-dna-protein hybrid if
> I am right ) . So there OL15 was not mentioned which made me wonder what
> is the difference on the same.
> On 17 Sep 2020 14:17, "Jiri Sponer" <sponer.ncbr.muni.cz> wrote:
>
>> Dear all,
>>
>> OL15 is the complete version.
>>
>> 1) It started from the ff99bsc0 version by adding DNA
>> specific modification of chi (chiOL4, Krepl et al. JCTC 2012),
>> important for example for quadruplexes. It is because it
>> was necessary to split the RNA and DNA force fields
>> due to contradicting requirements.
>>
>> 2) Then (Zgarbova et al JCTC 2013) eps/zeta has been modified,
>> resolving the B-DNA helical twist and BI/BII (ezOL1).
>>
>> 3) Finally, (Zgarbova et al 2015 JCTC)
>> the tricky beta dihedral (bOL1) has been reparametrized,
>> which further improves B-DNA and is essential for Z-DNA. Simultaneously,
>> to SIMPLIFY the name, it has been named
>> as OL15, which includes all the earlier modifications.
>> OL15 = Cornell et al. + ff99 + bsc0 + chiOL4 + ezOL1 + bOL1.
>>
>> Thus, OL15, as used, is basically a complete reparametrization
>> of the dihedral potentials of the seminal Cornell et al.
>> force field from 1995, published in a series of steps in 1999/2000, 2007,
>> 2012, 2013, and 2015.
>>
>> It is explained in the Zgarbova et al paper JCTC 2015
>> (Refinement of the SugarPhosphate Backbone Torsion Beta for
>> AMBER Force Fields Improves the Description of Z- and BDNA)
>> on p. 5724:
>> "We introduce a shorthand OL15 for the
>> combination of the bOL1, ezOL1 and chiOL4 dihedral modifications
>> (named after the city of Olomouc, parametrization version
>> 2015) ."
>>
>> So, OL15 includes everything.
>>
>> Best wishes, Jiri
>>
>> On Thu, 17 Sep 2020, David Cerutti wrote:
>>
>> Date: Thu, 17 Sep 2020 00:28:20 -0400
>>> From: David Cerutti <dscerutti.gmail.com>
>>> Reply-To: AMBER Mailing List <amber.ambermd.org>
>>> To: AMBER Mailing List <amber.ambermd.org>
>>> Subject: Re: [AMBER] Query on nucleic acid force fields
>>>
>>> I do not know what the special characters are in your titles there. I
>>> have
>>> listed for you the nucleic acid force fields that Amber offers as part of
>>> its installation--OL15 is among them but I do not know about the ff99bsc
>>> model. I have heard of something like this but you will need to look in
>>> the directories I described to see if there are perhaps some hints in the
>>> comments of those files. In leaprc.DNA.OL15, the preamble states:
>>>
>>> #
>>> # ----- NOTE: this is designed for PDB format 3!
>>> # Uses ff99bsc0+OL15 for DNA
>>> # (ff99): Wang et al. J. Comp. Chem. 21: 1049, 2000
>>> # (bsc0): Perez et al. Biophys J. 92: 3817, 2007
>>> # (OL15): Zgarbova et al. JCTC 11: 5723, 2015
>>> # load atom type hybridizations
>>> #
>>>
>>> So there is definitely a component of ff99bsc0 in there, but I don't know
>>> about the OL1 part you are talking about.
>>>
>>> Dave
>>>
>>>
>>> On Thu, Sep 17, 2020 at 12:15 AM Jenny 148 <jenny.rs140.gmail.com> wrote:
>>>
>>> Sir,
>>>> My major doubt is whether OL15 forcefield and ff99bsc0εζ OL1 forcefield
>>>> are
>>>> the same??
>>>> On 17 Sep 2020 09:05, "David Cerutti" <dscerutti.gmail.com> wrote:
>>>>
>>>> In order to source a nucleic acids force field you will state, in your
>>>>> leaprc, things like this:
>>>>>
>>>>> source leaprc.DNA.OL15
>>>>> source leaprc.RNA.OL3
>>>>>
>>>>> For DNA< you have choices of bsc1 and OL15--I am almost certain that
>>>>>
>>>> those
>>>>
>>>>> are substantially different, but check the literature from Cheatham
>>>>>
>>>> group.
>>>>
>>>>> For RNA, you have LJbb, OL3, ROC, Shaw, and YIL options. I cannot
>>>>> advise
>>>>> you on one model or another in this respect, but look in each of the
>>>>>
>>>> leaprc
>>>>
>>>>> files (located in ${AMBERHOME}/dat/leap/cmd/leaprc.[RD]NA.(option), and
>>>>> you
>>>>> should see lines like "loadOff DNA.OL15.lib" and "parm10 =
>>>>>
>>>> loadAmberParams
>>>>
>>>>> parm10.dat." The latter tells it to use torsion parameters from parm10,
>>>>> a
>>>>> central collection of valence terms from our protein force fields. You
>>>>> will find parm##.dat files in ${AMBERHOME}/dat/leap/parm/, and .lib
>>>>> (library) files in ${AMBERHOME}/dat/leap/lib/.
>>>>>
>>>>> HTH,
>>>>> Dave
>>>>>
>>>>>
>>>>> On Wed, Sep 16, 2020 at 9:12 AM Jenny 148 <jenny.rs140.gmail.com>
>>>>> wrote:
>>>>>
>>>>> Dear all,
>>>>>> The question might be really trivial. I would like to know if the OL15
>>>>>> forcefield and ff99bsc0εζ OL1 forcefield are the same. If not what is
>>>>>>
>>>>> the
>>>>
>>>>> difference. And how to source ff99bsc0εζ OL1? Thank you for your
>>>>>>
>>>>> time.
>>>>
>>>>>
>>>>>> --
>>>>>> Jenny R.S
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Received on Thu Sep 17 2020 - 03:00:02 PDT
