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*
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Received on Wed Sep 17 2014 - 05:00:02 PDT
