I'm going to simulate the protein in POPC bilayer. Do you suggest this
forcefield for this kind of bilayer too?
Thanks so much for your reply.
Sincerely,
Shima
________________________________
From: Thomas Piggot <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Sent: Tuesday, May 22, 2012 10:15 PM
Subject: Re: [gmx-users] forcefields for lipids
Hi Shima,
Yes, the phospholipid parameters are available to use. I am currently in the
process of uploading them to the Lipidbook website. If you check this website
soon they should be available to download (DPPE and POPE parameters and
bilayers are already there). For accessing them on Lipidbook the name of the
force field is the GROMOS-CKP lipid force field. The parameters are consistent
for use with the GROMOS 53A6 and GROMOS 54A7 protein force fields for
simulating membrane proteins systems. I should also note that the Kukol DMPC
and DPPC parameters (http://pubs.acs.org/doi/abs/10.1021/ct8003468) are also
consistent with these phospholipid parameters, if you wish to simulate mixed
lipid bilayers.
Cheers
Tom
Shima Arasteh wrote:
> Is this FF available for others to use?
>
> Thanks.
> Sincerely,
> Shima
> ------------------------------------------------------------------------
> *From:* Thomas Piggot <[email protected]>
> *To:* Discussion list for GROMACS users <[email protected]>
> *Sent:* Tuesday, May 22, 2012 7:39 PM
> *Subject:* Re: [gmx-users] forcefields for lipids
>
> Thanks Joakim,
>
> I will be very interested to see how these different lipids behave. This
> looks like it could be a really useful force field. We have also developed
> some parameters for PE, PG and Cardiolipin lipids which you might want to
> have a look at (for comparison with your ongoing parameter development).
> Details regarding the behaviour of these lipids are in the supporting info of
> this paper (http://pubs.acs.org/doi/abs/10.1021/jp207013v).
>
> Cheers
>
> Tom
>
> Joakim Jämbeck wrote:
> > Hi Tom,
> >
> > we have parameters for unsaturated tails now as well as for PE lipids
>ready for use, the manuscript for these have been submitted.
> >
> > PG and PS lipids are on the way and parameters for cholesterol and
>sphingomyelin are finished now and the manuscript should be finished
>relatively soon.
> >
> > Best,
> > J
> >
> >
> > On May 22, 2012, at 15:40 , [email protected]
><mailto:[email protected]> wrote:
> >
> >> Date: Tue, 22 May 2012 13:49:48 +0100
> >> From: Thomas Piggot <[email protected] <mailto:[email protected]>>
> >> Subject: Re: [gmx-users] forcefields for lipids
> >> To: Discussion list for GROMACS users <[email protected]
><mailto:[email protected]>>
> >> Message-ID: <[email protected]
><mailto:[email protected]>>
> >> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
> >>
> >> Hi Joakim,
> >>
> >> I am interested to know what other lipids this force field has been
>extended to include. Do you have parameters for unsaturated lipid tails and
>other classes of phospholipid (such as PE and PG)?
> >>
> >> Cheers
> >>
> >> Tom
>
> -- Dr Thomas Piggot
> University of Southampton, UK.
> --
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>
-- Dr Thomas Piggot
University of Southampton, UK.
--
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