[AMBER] MD of an elongated active site protein.

From: Saman Yousuf ali <saman.yousufali64.yahoo.com>
Date: Sat, 9 Jul 2016 14:58:02 +0000 (UTC)

Dear all,
I am interested to run MD simulation to look closer into the mode of interactions between different ligands and protein. My target protein is a homotetramer and I have selected it's chain A for my study. In literarture, It is mentioned that It has an elongated active site, which is primarily formed by a A chain and some residues from C-terminus D chain are also located close to it. In that case, I am using both chains for running MD. My question is, can I use chain A complex with ligand while chain D without ligand to mimic original system? or I have to use both chains in complex with ligands? Your help is appreciated.
(I am only interested to study chain A but due to elongated active site, I m also using D chain.)

Best Regards, Sarah
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Received on Sat Jul 09 2016 - 08:00:03 PDT
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