That's great Carlos, Congrats and thanks a lot for pointing it to us ...
Vlad
On 09/17/2014 01:31 PM, Carlos Simmerling wrote:
> for those interested in the topic of ff14SB and protein folding, our work
> on this was recently published in JACS:
> http://pubs.acs.org/doi/abs/10.1021/ja5032776
>
> On Fri, Sep 12, 2014 at 8:40 PM, Thomas Evangelidis <tevang3.gmail.com>
> wrote:
>
>> On 12 September 2014 16:43, Jason Swails <jason.swails.gmail.com> wrote:
>>
>>> On Fri, 2014-09-12 at 18:48 +0530, sunita.tifrh.res.in wrote:
>>>> Dear Guys,
>>>>
>>>> After going through the literature I find ff99SB*-ILDN is the one which
>>>> gives comparable result to the experimental observations.
>>>>
>>>> I am having Amber12 where leaprc of ff99SBildn, ff12SB etc are there
>> but
>>>> ff99SB*ildn is not there.
>>> I've never heard of this force field before. When I pulled up one of
>>> D.E. Shaw's papers mentioning ff99SB*ILDN [1], that force field had 3
>>> citations: ff99SB, another citation, and then the original citation for
>>> ff99SB-ILDN (i.e., there is no indication I see that this force field is
>>> any different than ff99SB-ILDN).
>>>
>>>
>> I don't like making bold statements, but in this case you are totally
>> wrong. The paper describing the backbone torsion modifications made in
>> ff99SB and ff03 by Best & Hummer (as Hannes correctly mentioned) is:
>>
>> http://pubs.acs.org/doi/abs/10.1021/jp901540t
>>
>> According to Scopus this paper has 180 citations, so I am surprised you
>> never heard of ff99sb* or ff03*. ff99sb*-ILDN is simply ff99sb* along with
>> the side chain torsion modification introduced by Shaw and co-workers.
>>
>> In my experience ff99sb* along with charmm22* are the golden standards used
>> by people that do metadynamics - and not only- with GROMACS. I tend to more
>> and more people to use these "star" force fields in the last years and I
>> bet there must be a good reason for that.
>>
>> As far as I am concerned, I do accelerated MD (in AMBER) and metadynamics
>> (in GROMACS) of intrinsically disordered proteins and I can say that I am
>> disappointed by the performance of ff12sb and ff99sb-nmr1-ildn. These seem
>> to overestimate the helical content of the cases I am working on. In
>> contrast, ff03w+TIP4P/2005 (another modified amber force field) which was
>> designed to yield more accurate helix-coil transitions, gives better
>> estimates of the secondary structure, at least for my cases. The latter
>> test was made by HREX simulations in GROMACS, which is very computer
>> demanding. I believe the addition of these modified amber force fields
>> (ff99sb*-ildn, ff03*, ff03w+TIP4P/2005) would be a great upgrade to the
>> AMBER arsenal. AMBER has the advantage to be faster in GPUs than GROMACS or
>> NAMD and also provides aMD, which is one of the least computer demanding
>> enhanced sampling methods. Unfortunately, I do not have the time, neither
>> the technical support to port myself these force fields into AMBER.
>>
>> Now, regarding Carlos' statement that ff14sb is better than ff99sb*-ildn, I
>> am curious to know the reasons that led him to that conclusion.
>>
>> best,
>> Thomas
>>
>>
>>
>>
>> --
>>
>> ======================================================================
>>
>> Thomas Evangelidis
>>
>> PhD student
>> University of Athens
>> Faculty of Pharmacy
>> Department of Pharmaceutical Chemistry
>> Panepistimioupoli-Zografou
>> 157 71 Athens
>> GREECE
>>
>> email: tevang.pharm.uoa.gr
>>
>> tevang3.gmail.com
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>> ===============================================================
>>
>> *Physics is the only real science. The rest are just stamp collecting.*
>>
>> *- Ernest Rutherford*
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 17 2014 - 05:30:03 PDT
