If you can get your original conformation into a pdb file and e.g.
leap> x = loadpdb lig.pdb
then the conformation should be preserved.
Bill
On 5/21/2012 8:11 PM, anyiphysics.gmail.com wrote:
> 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 - 20:30:03 PDT
