Hi <meta http-equiv="content-type" content="text/html; charset=utf-8">Anirban,<div>as far as I know the best force-field for membrane protein system is Charm36: it uses Charm27 for proteins but an improved parametrization for membrane lipids.</div>
<div>I don't know if the lipids part has been already ported in gromacs format, but is a trivial task you can do in 1-2 days.</div><div><br></div><div>Francesco<br><br><div class="gmail_quote">Il giorno 19 aprile 2012 08:32, Anirban Ghosh <span dir="ltr"><<a href="mailto:reach.anirban.ghosh@gmail.com">reach.anirban.ghosh@gmail.com</a>></span> ha scritto:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi ALL,<div><br></div><div>When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or DPPC etc.) which according to your experience is the most suited force-field in GROMACS that best retains the 7TM / secondary structures of the protein over long simulations? I have tried running with ff53a6 (as suggested in Justin's tutorial), but find that the helices in the bilayer tend to lose their helicity over time and turns into coils. ff43a2 seems to do the job somewhat better by retaining the helicity. Will ff43a1 work even better as the principle aim is to observe changes in the protein without losing its secondary structures? Your experience please.</div>
<div>Thanks a lot in advance.</div><div><br></div><div><br></div><div>Regards,</div><div><br></div><div>Anirban</div>
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