Here is another paper related to the secondary structure propensity
of different force field.
Are current Molecular Dynamics FFs too helical? Best et al:
BiophysJ-2008
doi:10.1529/biophysj.108.132696
Note that these papers do not report the unstability of helices in
proteins!
On Jan 22, 2010, at 1:03 AM, Krzysztof Mlynarczyk wrote:
Thank you!!!
The evidence presented in this paper is stunning. It also stresses
the importance of using the electrostatics treatment that was
originally used for development of a particular force field, e.g.
reaction field in case of G96 - the popular PME in connection with
G53a6 results in even stronger beta sheet bias. This way using this
force field is out of the question, unless until corrections are
made and tested. I need a different solution for my problem.
Christopher
2010/1/21 Erik Marklund <er...@xray.bmc.uu.se>
It is documented. Have a look at this one:
Dirk Matthes and Bert L. de Groot. Secondary structure propensities
in peptide folding simulations: A systematic comparison of molecular
mechanics interaction schemes. Biophys. J. 97:599-608 (2009)
Erik
XAvier Periole skrev:
The instability of helices with the G53a6 force field is definitely
real
and unfortunately not documented. Some people are working on it ...
I would advise to be very carefull in interpreting results with this
FF.
XAvier.
On Jan 21, 2010, at 2:13 PM, Justin A. Lemkul wrote:
Krzysztof Mlynarczyk wrote:
2010/1/21 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Krzysztof Mlynarczyk wrote:
2. If not, is there any way to derive the proper parameters for
the force field of my choice using the lipid parameters from
Peter Tieleman's website or e.g. the parameters published by
Andreas Kukol for G53a6?
I don't see why you need to do such reverse engineering. The Kukol
parameters for lipids under 53a6 can be directly combined with a
G53a6 protein without any issues; I believe that was the purpose of
the whole new derivation :)
I received a message that G53a6 is beta-sheet biased and alpha
helices do not perform as well as they should. My protein contains 7
transmembrane helices, that's why I'm worried.
Is this published somewhere? That would be important information.
Perhaps this is the case for model peptides or short fragments, but
I have certainly done a number of simulations using 53a6 with well-
folded globular proteins and I do not see any such instability
(i.e., alpha->beta conversion or unwinding of alpha-helices). I do
believe it is possible in certain scenarios, but I don't know that a
large 7TM protein like yours would suffer adversely.
I know that there are changes between parameter sets both in non-
bonded and bonded terms and one rtp entry will probably not work
well when pasted into a different force field from the same family.
G96 family uses symbols like gd_5 that are substituted by
appropriate parameters later through the use of preprocessor. While
it is possible to find that gd_5 is the same as gd_15 in another
version of G96 and substitute those symbols in topologies, the
changes in non bonded parameters still can spoil what was working
well elsewhere. That's why I was also asking for some checked and
ready-to-use topologies for a particular force field.
Many of the bonded parameters carry over between force fields, but
certainly new entries were created between 43a2 and 53a6, so yes,
some re-working would likely be necessary. There is a lipid 43a2
parameter set on the User Contribution site, like I said before, I
just don't know if there is a reference for it.
As an aside, you are quite right that multiple force fields within
the same simulation is incorrect. However, the Berger lipid
parameters may be an exception to this rule, since they are really a
hybridized version of OPLS-UA and Gromos87 parameters (some of which
were modified anyway), so they really don't belong to any one
particular force field. The Berger/G87 combination is widely used,
but essentially amounts to the following: lipid interactions are
Berger-Berger or OPLS-OPLS interactions, while protein-lipid
interations are Berger-G87, and protein-protein interactions are
G87-G87. You can see quite quickly why things become complicated!
Based on a discussion I had with Dr. Tieleman, it seems to be
reasonable to use the G96 parameter set of your choice in
conjunction with lipid.itp (Berger lipids), although other
approaches may be more rigorously correct (pure G96 parameters such
as those by Kukol, pure OPLS recently derived by Ulmschneider, or
the modifications to the Berger parameters from the Tieleman group,
to name a few). If you want to use a G96-lipid.itp combination, I
created a tutorial that teaches you how to build the system and
properly prepare the topology. It is linked from the Tutorials page
of the Gromacs site.
I found this tutorial earlier and was also in doubt if this approach
was correct. But if it works, perhaps I should give it a try.
I gotta make a _good_ decision in the end...
As do we all :) My work with G53a6+Berger has thus far been quite
reliable, from everything I can measure, but that certainly does not
preclude the possibility (even likelihood) that there are better
procedures out there, like those I quoted above, and certainly
others (CHARMM is also popular for membrane proteins, but Gromacs
will only *officially* support CHARMM as of version 4.1).
-Justin
Christopher
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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