[gmx-users] Lipid parameters for GROMOS96 force fields

XAvier Periole x.periole at rug.nl
Fri Jan 22 09:36:35 CET 2010 

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 <erikm at 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 <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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>
> -- 
> -----------------------------------------------
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
>
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