Thanks for the references Jason. Banas 2010 does not show how the
revisions of chi torsions are made. It uses two revisions (that is not
published yet) and test those two as well as my revision on hairpin
structures. They say in the paper that they used deoxyribonucleosides, not
ribonucleosides in the chi revisions. They conclude that revision of chi
is crucial - which I showed in my paper:
"Re-parameterization of RNA CHI Torsion Parameters for the AMBER Force
Field and Comparison to NMR Spectra for Cytidine and Uridine," I.
Yildirim, H.A. Stern, S.D. Kennedy, J.D. Tubbs, and D.H. Turner, J. Chem.
Theory and Comput. 6, 1520-1531 (2010).
I am not going argue on those parameter sets. I did some calculations
using those parameters on some systems and concluded that OL-DFT cannot be
used in at least RNA systems. It seems that the parameters in ff10 is OL,
not OL-DFT, but still how the revisions are made is not clear because the
paper is not published.
I am really curious now what the designers of that force field will say
about this. Even though I am the first to publish and show the importance
of the chi revision, ff10 with the references Jason gave imply that they
found out the problem on chi torsion. Without giving credit to someone who
shows the problem with a solution is nothing but injustice.
As I wrote before, I spend my whole phd time to figure out what was
causing the problems to the single strand RNAs and solved this problem at
the end of my phd time. The original revision paper is the one I gave
above. I am waiting to hear from JPC B for the single strand GACC RNA
paper I submitted.
Looking forward to hear from the designers of the ff10 force field as
well as anyone who wants to comment on this issue.
Sincerely,
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Department of Chemistry - 2145 Sheridan Road =
= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
=
http://www.pas.rochester.edu/~yildirim/ =
-----------------------------------------------------------
On Sun, 27 Mar 2011, Jason Swails wrote:
> Hi Ilyas,
>
> The extent of my knowledge on these parameters are what I read in the
> manual. The paragraph on "chi.OL3" corrections are:
>
> 3. ff99bsc0 and chi.OL3 for nucleic acids. The nucleic acid force fields
> have recently been updated from those in ff99, in order to address a
> tendency of DNA double helices to convert (after fairly long simulations) to
> extended forms in the \alpha and \gamma backbone torsion angles.(Perez07)
> Another change updates the glyocosidic torsional parameters for RNA.
> (Banas10)
>
> The citations listed there are
>
> .Article{Perez07,
> author = {Perez, A. and Marchan, I. and Svozil, D. and Sponer, J. and
> Cheatham, T.E. and Laughton, C.A. and Orozco, M.},
> title = {{Refinement of the AMBER Force Field for Nucleic Acids: Improving
> the Description of alpha/gamma Conformers}},
> journal = {Biophys. J.},
> volume = {92},
> pages = {3817-3829},
> year = {2007}
> }
>
> and
>
> .Article{Banas10,
> author = {Ban\'{a}\v{s}, P. and Hollas, D. and Zgarbov\'{a}, M. and
> Jurecka,
> P. and Orozco, M. and Cheatham, III, T.E. and \v{S}poner, J. and Otyepka,
> M.},
> title = {{Performance of molecular mechanics force fields for RNA
> simulations: Stability of UUCG and GNRA hairpins}},
> journal = {J. Chem. Theory. Comput.},
> volume = {6},
> pages = {3836-3849},
> year = {2010}
> }
>
> Outside of this, I don't know exactly what parameters were put into ff10.
> Hopefully some of the designers of that force field can chime in here and
> see if we've forgotten to add a reference or something.
>
> All the best,
> Jason
>
> On Sun, Mar 27, 2011 at 11:49 AM, <yildirim.pas.rochester.edu> wrote:
>
>> I've published a paper regarding revision of chi torsion for RNA last
>> year, which I think most of you are aware of. We tested it on the smallest
>> structures; mononucleosides of A,G,C,U. It was even tested on hairpin
>> structures in Banas et al. 2010 paper. I have spent almost my whole phd
>> year to figure out why RNA single strands were not behaving right. At the
>> end I revised the chi torsions, and tested on (both computationally and
>> experimentally) on mononucleosides. We did a similar analysis on single
>> strand GACC tetramer RNA and submitted to JPC B to show that chi revision
>> is important. There is another paper in line to be submitted that shows
>> its importance on free energy predictions.
>>
>> I would like to know if my work has been ignored and chi1.OL3 (which I am
>> not sure if it is even published or published before my work) is included
>> in ff10.
>>
>> Sincerely,
>>
>> Ilyas Yildirim, Ph.D.
>> -----------------------------------------------------------
>> = Department of Chemistry - 2145 Sheridan Road =
>> = Northwestern University - Evanston, IL 60208 =
>> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
>> = http://www.pas.rochester.edu/~yildirim/ =
>> -----------------------------------------------------------
>>
>>
>> On Sun, 27 Mar 2011, Jason Swails wrote:
>>
>>> According to the manual, ff10 has the chi1.OL3 modifications. It should
>> be
>>> part of parm10.dat.
>>>
>>> I'm in the process of checking this out now ;).
>>>
>>> All the best,
>>> Jason
>>>
>>> On Sun, Mar 27, 2011 at 11:23 AM, <yildirim.pas.rochester.edu> wrote:
>>>
>>>> I have a question regarding the amber ff10 force field. Is there any
>>>> revision for chi torsions? If yes, which parameter set is used?
>>>>
>>>> Ilyas Yildirim, Ph.D.
>>>> -----------------------------------------------------------
>>>> = Department of Chemistry - 2145 Sheridan Road =
>>>> = Northwestern University - Evanston, IL 60208 =
>>>> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
>>>> = http://www.pas.rochester.edu/~yildirim/ =
>>>> -----------------------------------------------------------
>>>>
>>>>
>>>> On Sun, 27 Mar 2011, Jason Swails wrote:
>>>>
>>>>> On Sun, Mar 27, 2011 at 4:39 AM, case <case.biomaps.rutgers.edu>
>> wrote:
>>>>>
>>>>>> Hi everyone:
>>>>>>
>>>>>> I have posted a new release candidate here:
>>>>>>
>>>>>> http://ambermd.org/downloads/AmberTools.26mar11.tar.bz2
>>>>>>
>>>>>> Still needed:
>>>>>>
>>>>>> 1. Proofreading of Users' Manual.
>>>>>> 2. Testing of the ff10 force field files
>>>>>>
>>>>>
>>>>> How would we check that the RNA/DNA force fields act as advertised?
>> Are
>>>> the
>>>>> chi.OL3 parameters found in a separate frcmod file somewhere that we
>>>> could
>>>>> add onto ff99bsc0?
>>>>>
>>>>> 3. Minor tweaks to the tests, esp. MMPBSA.py
>>>>>>
>>>>>
>>>>> What tweaks are needed here?
>>>>>
>>>>>
>>>>>>
>>>>>> I know lots of people are at ACS, but any help you can give
>> (especially
>>>> for
>>>>>> item 2) would help us get this baby out the door.
>>>>>>
>>>>>> ...thanks...dac
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER-Developers mailing list
>>>>>> AMBER-Developers.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Jason M. Swails
>>>>> Quantum Theory Project,
>>>>> University of Florida
>>>>> Ph.D. Candidate
>>>>> 352-392-4032
>>>>> _______________________________________________
>>>>> AMBER-Developers mailing list
>>>>> AMBER-Developers.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER-Developers mailing list
>>>> AMBER-Developers.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>>
>>>
>>>
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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Received on Sun Mar 27 2011 - 16:00:02 PDT
