[gmx-users] Lipid parameters for GROMOS96 force fields

[Erik Marklund]

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)

Erik

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.
>
> 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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>


-- 
-----------------------------------------------
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