[gmx-users] Lipid parameters for GROMOS96 force fields

[Krzysztof Mlynarczyk]

Hi,

I already have both your publication and supplementary material from your
website. The files were also submitted to Gromacs user contribution section:
http://www.gromacs.org/@api/deki/files/23/=LipidsForGro96_53a6.zip
Have you noticed anything suspicious in alpha helix behaviour in G53a6 force
field?

Christopher

2010/1/21 Kukol, Andreas <a.kukol at herts.ac.uk>

> Hi,
>
> Lipid parameters for Gromos96 53a6 are available based on the publication
>
> Kukol, A., 2009. Lipid models for united-atom molecular dynamics
> simulations of proteins. J. Chem. Theor. Comput.,5(3), 615-626.
>
> Unfortunately, I did not manage yet to upload it on the new Gromacs
> website. Please contact me off the list for the itp-files for DPPC, DMPC,
> POPC and POPG for 53a6 forcefield.
>
> Andreas
>
>
> > -----Original Message-----
> > From: gmx-users-bounces at gromacs.org [mailto:
> gmx-users-bounces at gromacs.org]
> > On Behalf Of Justin A. Lemkul
> > Sent: 21 January 2010 01:36
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] Lipid parameters for GROMOS96 force fields
> >
> >
> >
> > 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
> > >>
> > >
> >
> > --
> > ========================================
> >
> > 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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