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.peri...@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 <jalem...@vt.edu <mailto: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. >> >> 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 >> >> ======================================== >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php