Hi amber users,
I'm trying to simulate a protein with an AMP-bound ligand. I went through
all the steps following the antechamber tutorial and added all the
parameters to this ligand. However, I found that the structure of my ligand
changed completely after I saved it as a pdb file using Leap. I heard that
in antechamber, sqm will optimize (minimize) the structure and change the
conformation of the ligand. Is it true? How can I maintain the original
conformation? Thank you very much.
Yi An
Graduate Student
Chemistry Department
Texas A&M University
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Received on Mon May 21 2012 - 20:30:02 PDT
