AMBER Archive (2008)

Subject: AMBER: ligand complexed simulation

From: Siddharth Rastogi (
Date: Fri Jun 20 2008 - 02:14:18 CDT

Dear AMBER users,

I am studying the dynamics of a protein in a complexed form.
The crystal structure of the protein (from PDB) contains ligand with TWOchains.
Indeed these two chains are identical and mirror images of each other.

Now the question is to run the simulation , whether I need to consider both
the chains of the ligand OR a single chain of the ligand?
If I will consider a single chain, whether it will affect the simulation
result ?

Any suggestions are most welcome.
Thanks in advance.


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