AMBER: MD on protein-ligand interaction

From: Fenghui Fan <>
Date: Thu, 14 Sep 2006 07:04:20 -0700 (PDT)

Dear all,

When we prepare the files for protein-ligand
interaction MD, supposing we have the original
protein-ligand complex PDB file, and then we prepare
the ligand PDB file from the original protein-ligand
complex PDB file for antechamber, the ligand pdb file
may contain more atoms (H atoms for example) than the
original ligand cooordinates in the protein-ligand PDB
files. Ina adition, the values of the coordinates will
be significantly different from the values of the
coordinates, although it still adopt the same

Should we change the ligand coordinateds in the
original protein-ligand pdb file to the newly created
ligand PDB file? Is it necessary? How can we do that?

I am looking forward to getting your reply.

Best regards.

Fenghui Fan

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Received on Sun Sep 17 2006 - 06:07:12 PDT
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