Hi, I am planing to use 53a6 ff for my membrane protein system. And I can use Kukol 2009 lipid or Roger 2010 lipids so I wonder is there any problem about 53a6 force field and what is the most suitable force field for membrane protein systems?
1) Kukol, A., 2009. Lipid models for united-atom molecular dynamics simulations of proteins 2) D Poger, WF Van Gunsteren, 2010. A new force field for simulating phosphatidylcholine bilayers. Thanks. Deniz. On Fri, Jan 22, 2010 at 11:36 AM, XAvier Periole <x.peri...@rug.nl> wrote: > > 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 <er...@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 <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 >>> >> >> >> -- >> ----------------------------------------------- >> 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 >> er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys >> >> -- >> 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 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 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-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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