[gmx-users] Lipid parameters for GROMOS96 force fields
mitomaster at gmail.com
Thu Jan 21 13:12:26 CET 2010
2010/1/21 Justin A. Lemkul <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.
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.
> 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...
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