AMBER Archive (2007)

Subject: AMBER: PDBs

From: Beale, John (jbeale_at_stlcop.edu)
Date: Tue Apr 17 2007 - 07:22:42 CDT

I am trying to create the files of a ligand bound to a protein for
xleap. I have successfully used Antechamber to generate the prmtop and
inpcrd files, plus a pdb, for my ligand. I have the pdb file of the
protein. My question is this: how do I merge the two files so that the
ligand becomes associated with the correct site on the protein? If I use
Sybyl to generate a pdb file of the complex, I assume that I will
somehow have to replace the content in the Sybyl pdb file with the
antechamber content. I guess what I am trying to ask in a roundabout way
is how do I build a pdb file of a complex using a ligand from
antechamber and the pdb file of the protein?

 

John Beale

 

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