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 Fri Sep 12 2014 - 18:00:02 PDT
