[gmx-users] Lipid parameters for GROMOS96 force fields
erikm at xray.bmc.uu.se
Thu Jan 21 14:32:12 CET 2010
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)
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.
> On Jan 21, 2010, at 2:13 PM, Justin A. Lemkul wrote:
>> Krzysztof Mlynarczyk wrote:
>>> 2010/1/21 Justin A. Lemkul <jalemkul at vt.edu <mailto: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.
>> 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 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
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at http://www.gromacs.org/search before
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at 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
erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
More information about the gromacs.org_gmx-users