Hi ALL,<div><br></div><div>Thanks a lot for the replies. </div><div>By long simulation I mean 500 ns to 1000 ns. Has anybody tried with the ff43a1 with any membrane protein?</div><div><br></div><div>Thanks,</div><div><br></div>
<div>Anirban<br><br><div class="gmail_quote">On Fri, Apr 20, 2012 at 3:26 AM, Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu">pcl@uab.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Define long simulations? CHARMM27/36 in the sub-100ns timescale works for us.<br>
<br>
The following paper:<br>
Vanni, S., Neri, M., Tavernelli, I., and Rothlisberger, U.: Predicting Novel Binding Modes of<br>
Agonists to Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations. PLoS<br>
Comput Biol 7, e1001053 (2011)<br>
<br>
Uses Amber99SB over 500-800+ns for their beta2-adrenergic receptor system.<br>
<div class="HOEnZb"><div class="h5"><br>
On 2012-04-19 12:02:36PM +0530, Anirban Ghosh wrote:<br>
> Hi ALL,<br>
><br>
> When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or<br>
> DPPC etc.) which according to your experience is the most suited<br>
> force-field in GROMACS that best retains the 7TM / secondary structures of<br>
> the protein over long simulations? I have tried running with ff53a6 (as<br>
> suggested in Justin's tutorial), but find that the helices in the bilayer<br>
> tend to lose their helicity over time and turns into coils. ff43a2 seems to<br>
> do the job somewhat better by retaining the helicity. Will ff43a1 work even<br>
> better as the principle aim is to observe changes in the protein without<br>
> losing its secondary structures? Your experience please.<br>
> Thanks a lot in advance.<br>
><br>
><br>
> Regards,<br>
><br>
> Anirban<br>
<br>
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Peter C. Lai | University of Alabama-Birmingham<br>
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