[gmx-users] Lipid parameters for GROMOS96 force fields

[XAvier Periole]

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 <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
>
>> 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
>
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