[AMBER] Simulation with Protein, cofactor and Ligand

From: Prasanth G, Research Scholar <prasanthghanta.sssihl.edu.in>
Date: Fri, 26 Apr 2019 00:11:05 +0530

Dear all,

I am interested in carrying out an amber simulation with protein along with
a cofactor, Glutathione ( C10 H17 N3 O6 S) and a ligand.
Could you please, let me know, if there is any protocol to be followed for
this kind of simulation.
In my humble opinion,
we need to-
1) use antechamber and make the topology and coordinate files for both
cofactor and the ligand
2) prepare protein using H++ server
3) combine all the three into a complex using tleap
4) carry simulation.

My question is, do we need to use any special restraints for the cofactor?
If yes, is it required even during the production phase of the simulation
or is it sufficient during the minimization and equilibration phases?
Request you to help me in this regard.
Thank you.

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Received on Thu Apr 25 2019 - 12:00:02 PDT
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