[gmx-users] Best Force Field for a Membrane Protein
Peter C. Lai
pcl at uab.edu
Thu Apr 19 23:56:16 CEST 2012
Define long simulations? CHARMM27/36 in the sub-100ns timescale works for us.
The following paper:
Vanni, S., Neri, M., Tavernelli, I., and Rothlisberger, U.: Predicting Novel Binding Modes of
Agonists to Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations. PLoS
Comput Biol 7, e1001053 (2011)
Uses Amber99SB over 500-800+ns for their beta2-adrenergic receptor system.
On 2012-04-19 12:02:36PM +0530, Anirban Ghosh wrote:
> Hi ALL,
> 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.
> Thanks a lot in advance.
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Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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