2010/1/21 Justin A. Lemkul <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. 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... Christopher
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