[gmx-users] Lipid parameters for GROMOS96 force fields

Thu Jan 21 17:50:01 CET 2010

Hello,
I'm very happy that so many people contributed to the subject of the
(in)validity of using G53a6 for alpha helical proteins.
Thank you for the links.
I know now that I certainly should use a different force field from the
GROMOS96 family, which maintains alpha helices where they should be and
there are tested parameters for the lipid of my choice, POPC. I could merge
lipid.itp with this force field's files and use a ready topology - that's
one option...

Christopher

2010/1/21 Tsjerk Wassenaar <tsjerkw at gmail.com>

> Hi,
>
> Well, we have compared the G53a5/6 force field with the 43a2 one and
> found consistently larger radii of gyration and higher RMSDs,
> suggesting decreased stability. There's a thorough account of it in my
> thesis (
> http://dissertations.ub.rug.nl/FILES/faculties/science/2006/t.a.wassenaar/04emb_c4.pdf
> )
> and it's been published in JPCB in 2007 (DOI: 10.1021/jp068580v).
>
> Cheers,
>
> Tsjerk
>
> On Thu, Jan 21, 2010 at 2:24 PM, XAvier Periole <x.periole at rug.nl> wrote:
> >
> > 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 <jalemkul at vt.edu <mailto:jalemkul at 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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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
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