AMBER Archive (2006)

Subject: AMBER: pqr file

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Thu Nov 16 2006 - 10:43:55 CST

Does anyone know of any way to create a pqr file of a ligand that is represented
by the GAFF? I've tried using pdb2pqr but had some trouble. Someone else from
their user group had the same issue and the explanation was as follows:

 "P.S.: Of course, you can assign charges with the GAFF (Generalised Amber Force
 Field) and do the editing in the AMBER.dat for your ligand. This is a tedious
 workaround for your case, but if you only have one ligand, this is a
 reasonable and pragmatic approach."

Does anyone have experience doing this? I'm not sure exactly what he means. I
appologize for the slightly off AMBER question... thanks in advance for anyones
cooperation.

Thanks,
SETH
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