Dear Michael,
Recently I found this paper, might be useful.
Good luck,
Ofir.
Methods Mol Biol. 2015 ; 1215: 253–287. doi:10.1007/978-1-4939-1465-4_12.
Accelerated Molecular Dynamics and Protein Conformational
Change: A Theoretical and Practical Guide Using a Membrane
Embedded Model Neurotransmitter Transporter
Patrick C. Gedeon, James R. Thomas, and Jeffry D. Madura
Dr. Ofir Tal, PhD
Structural Bioinformatics
Bioinformatics Knowledge Unit - BKU
http://bku.technion.ac.il/
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of TechnologyHaifa 32000, ISRAEL
pantufel.technion.ac.il
> From: michael.shokhen.biu.ac.il
> To: AMBER.ambermd.org
> Date: Thu, 31 Mar 2016 10:07:56 +0000
> Subject: Re: [AMBER] aMD simulation of membrane protein ?
>
> Both - protein and membrane must be accounted as solute
> in aMD parameters settings.
>
> Michael
>
>
>
>
>
> ________________________________________
> From: Michael Shokhen <michael.shokhen.biu.ac.il>
> Sent: Wednesday, March 30, 2016 1:18 PM
> To: AMBER.ambermd.org
> Subject: [AMBER] aMD simulation of membrane protein ?
>
> Dear Amber experts,
>
> I have Amber14 and AmberTools15, and I want to apply aMD
> accelerated MD for the simulation of membrane protein.
>
> The AMBER "Advanced Tutorial 22 Introduction" describes
> an example of water solvated protein aMD simulation,
> so I have some questions about the aMD protocol application
> for membrane proteins.
>
> 1.
> The parameter setting in the tutorial defines E(dih) and Alpha(dih)
> for solute atoms only that is protein in the tutorial:
>
>
> c) EthreshD: E(dih)=595 kcal mol-1 + (4kcal mol-1 residue-1 * 58 solute residues) = 827 kcal mol-1
>
> d) alphaD: Alpha(dih)=(1/5)*(4kcal mol-1 residues-1 * 58 solute residues) = 46.4 kcal mol-1
>
> Do I need to extend the E(dih) and Alpha(dih) setting on membrane lipid molecules also?
>
>
> 2. I would appreciate if somebody address me to any published
> amber protocol of membrane protein aMD simulation.
>
> Thank you,
> Michael
>
>
>
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Received on Thu Mar 31 2016 - 07:30:03 PDT
