Hi,<br><br>I already have both your publication and supplementary material from your website. The files were also submitted to Gromacs user contribution section:<br><a href="http://www.gromacs.org/@api/deki/files/23/=LipidsForGro96_53a6.zip">http://www.gromacs.org/@api/deki/files/23/=LipidsForGro96_53a6.zip</a><br>
Have you noticed anything suspicious in alpha helix behaviour in G53a6 force field?<br><br>Christopher<br><br><div class="gmail_quote">2010/1/21 Kukol, Andreas <span dir="ltr"><<a href="mailto:a.kukol@herts.ac.uk">a.kukol@herts.ac.uk</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br>
<br>
Lipid parameters for Gromos96 53a6 are available based on the publication<br>
<br>
Kukol, A., 2009. Lipid models for united-atom molecular dynamics simulations of proteins. J. Chem. Theor. Comput.,5(3), 615-626.<br>
<br>
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.<br>
<font color="#888888"><br>
Andreas<br>
</font><div><div></div><div class="h5"><br>
<br>
> -----Original Message-----<br>
> From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>]<br>
> On Behalf Of Justin A. Lemkul<br>
> Sent: 21 January 2010 01:36<br>
> To: Discussion list for GROMACS users<br>
> Subject: Re: [gmx-users] Lipid parameters for GROMOS96 force fields<br>
><br>
><br>
><br>
> Justin A. Lemkul wrote:<br>
> ><br>
> ><br>
> > Krzysztof Mlynarczyk wrote:<br>
> >> Hello,<br>
> >><br>
> >> On Peter Tieleman's website we can find topologies for various popular<br>
> >> lipids. However those seem to be valid for the deprecated GROMOS87<br>
> >> force field. The g96_lipids.itp file is still unavailable. I'd like to<br>
> >> run a simulation of 7TM protein embedded into POPC membrane. G43a2x<br>
> >> seems to be a reasonable choice for this purpose. I still need the<br>
> >> parameters for my lipids. I am aware that combining parameters from<br>
> >> different force fields might lead to a disaster, that's why I want to<br>
> >> ask you:<br>
> >> 1. Do you know any papers where POPC membrane and G43a2 force field<br>
> >> was used?<br>
> ><br>
> > I've not seen one, because it has been known for some time that early<br>
> > Gromos96 parameter sets did not reproduce long alkyl chain properties<br>
> > particularly well.<br>
> ><br>
><br>
> Quick amendment - modifications to 43a2 and 45a3 have been made to better<br>
> reproduce lipid properties. Both are available for download on the Gromacs<br>
> site<br>
> and you can probably track down the references, as well.<br>
><br>
> Sorry, read that one wrong the first time :)<br>
><br>
> -Justin<br>
><br>
> >> 2. If not, is there any way to derive the proper parameters for the<br>
> >> force field of my choice using the lipid parameters from Peter<br>
> >> Tieleman's website or e.g. the parameters published by Andreas Kukol<br>
> >> for G53a6?<br>
> >><br>
> ><br>
> > I don't see why you need to do such reverse engineering. The Kukol<br>
> > parameters for lipids under 53a6 can be directly combined with a G53a6<br>
> > protein without any issues; I believe that was the purpose of the whole<br>
> > new derivation :)<br>
> ><br>
> > As an aside, you are quite right that multiple force fields within the<br>
> > same simulation is incorrect. However, the Berger lipid parameters may<br>
> > be an exception to this rule, since they are really a hybridized version<br>
> > of OPLS-UA and Gromos87 parameters (some of which were modified anyway),<br>
> > so they really don't belong to any one particular force field. The<br>
> > Berger/G87 combination is widely used, but essentially amounts to the<br>
> > following: lipid interactions are Berger-Berger or OPLS-OPLS<br>
> > interactions, while protein-lipid interations are Berger-G87, and<br>
> > protein-protein interactions are G87-G87. You can see quite quickly why<br>
> > things become complicated!<br>
> ><br>
> > Based on a discussion I had with Dr. Tieleman, it seems to be reasonable<br>
> > to use the G96 parameter set of your choice in conjunction with<br>
> > lipid.itp (Berger lipids), although other approaches may be more<br>
> > rigorously correct (pure G96 parameters such as those by Kukol, pure<br>
> > OPLS recently derived by Ulmschneider, or the modifications to the<br>
> > Berger parameters from the Tieleman group, to name a few). If you want<br>
> > to use a G96-lipid.itp combination, I created a tutorial that teaches<br>
> > you how to build the system and properly prepare the topology. It is<br>
> > linked from the Tutorials page of the Gromacs site.<br>
> ><br>
> > -Justin<br>
> ><br>
> >> Thank you in advance,<br>
> >> Christopher<br>
> >><br>
> ><br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
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</div></div></blockquote></div><br>