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 - 03:30:03 PDT
