[gmx-users] Lipid parameters for GROMOS96 force fields
tsjerkw at gmail.com
Thu Jan 21 14:34:20 CET 2010
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
and it's been published in JPCB in 2007 (DOI: 10.1021/jp068580v).
On Thu, Jan 21, 2010 at 2:24 PM, XAvier Periole <x.periole at 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.
> 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
>>> 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
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Tsjerk A. Wassenaar, Ph.D.
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