[gmx-users] Lipid parameters for GROMOS96 force fields

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> Krzysztof Mlynarczyk wrote:
>> Hello,
>>
>> On Peter Tieleman's website we can find topologies for various popular 
>> lipids. However those seem to be valid for the deprecated GROMOS87 
>> force field. The g96_lipids.itp file is still unavailable. I'd like to 
>> run a simulation of 7TM protein embedded into POPC membrane. G43a2x 
>> seems to be a reasonable choice for this purpose. I still need the 
>> parameters for my lipids. I am aware that combining parameters from 
>> different force fields might lead to a disaster, that's why I want to 
>> ask you:
>> 1. Do you know any papers where POPC membrane and G43a2 force field 
>> was used?
> 
> I've not seen one, because it has been known for some time that early 
> Gromos96 parameter sets did not reproduce long alkyl chain properties 
> particularly well.
> 

Quick amendment - modifications to 43a2 and 45a3 have been made to better 
reproduce lipid properties.  Both are available for download on the Gromacs site 
and you can probably track down the references, as well.

Sorry, read that one wrong the first time :)

-Justin

>> 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 :)
> 
> 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.
> 
> -Justin
> 
>> Thank you in advance,
>> Christopher
>>
> 

-- 
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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

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