[gmx-users] Lipid parameters for GROMOS96 force fields
x.periole at rug.nl
Thu Jan 21 14:24:21 CET 2010
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
>> 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
>> parameters for lipids under 53a6 can be directly combined with a
>> G53a6 protein without any issues; I believe that was the purpose
>> 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
>> were modified anyway), so they really don't belong to any one
>> particular force field. The Berger/G87 combination is widely
>> 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
>> as those by Kukol, pure OPLS recently derived by Ulmschneider, or
>> the modifications to the Berger parameters from the Tieleman
>> 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
>> 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
>> 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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