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
>>>>
>>>>
>>>> _______________________________________________
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>>>> 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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>> AMBER-Developers.ambermd.org
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>>
>
>
>
> --
> 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 - 12:00:02 PDT
