Dear Amber users,
I am trying to set-up a metal-bound membrane protein system for accelerated
MD simulations, with initial 100 ns of cMD simulations. With regard to
this, I have a number of queries and I will be grateful if you could help
me with it.
1. The protein bear a sodium binding site, where the Na+ ion make five
co-ordinate bond with protein residues and water molecules. Which ion-model
will be better suite in this system? Is there any cationic dummy atom model
parameters available for sodium ion?
2. What all should I consider while building up a ion-bound membrane
protein system for simulating with aMD protocol?
Any help would be highly appreciated
Thanks in advance
Anu
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Received on Mon Dec 11 2017 - 02:00:02 PST
