<br><br><div class="gmail_quote">2010/1/21 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Krzysztof Mlynarczyk wrote:<br>
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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?<br>
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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 :)<br>
</blockquote><div><br>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. <br>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.<br>
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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!<br>
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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.<br>
<font color="#888888"><br></font></blockquote><div>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. <br>I gotta make a _good_ decision in the end...<br>
<br>Christopher<br></div></div><br>