[gmx-users] Lipid parameters for GROMOS96 force fields

Deniz KARASU karasudeniz at gmail.com
Sun Aug 8 12:43:12 CEST 2010 

Hi,

I am planing to use 53a6 ff for my membrane protein system. And I can
use Kukol 2009 lipid or Roger 2010 lipids  so I wonder is there any
problem about 53a6 force field and what is the most suitable force
field for membrane protein systems?

1) Kukol, A., 2009. Lipid models for united-atom molecular dynamics
simulations of proteins
2) D Poger, WF Van Gunsteren,  2010.  A new force field for simulating
phosphatidylcholine bilayers.

Thanks.
Deniz.

On Fri, Jan 22, 2010 at 11:36 AM, XAvier Periole <x.periole at rug.nl> wrote:
>
> Here is another paper related to the secondary structure propensity
> of different force field.
> Are current Molecular Dynamics FFs too helical? Best et al: BiophysJ-2008
> doi:10.1529/biophysj.108.132696
> Note that these papers do not report the unstability of helices in proteins!
> On Jan 22, 2010, at 1:03 AM, Krzysztof Mlynarczyk wrote:
>
> Thank you!!!
> The evidence presented in this paper is stunning. It also stresses the importance of using the electrostatics treatment that was originally used for development of a particular force field, e.g. reaction field in case of G96 - the popular PME in connection with G53a6 results in even stronger beta sheet bias. This way using this force field is out of the question, unless until corrections are made and tested. I need a different solution for my problem.
>
> Christopher
>
> 2010/1/21 Erik Marklund <erikm at xray.bmc.uu.se>
>>
>> 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
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>>
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