AMBER Archive (2006)

Subject: Re: AMBER: pqr file

From: David A. Case (case_at_scripps.edu)
Date: Thu Nov 16 2006 - 10:53:46 CST

On Thu, Nov 16, 2006, Seth Lilavivat wrote:

> Does anyone know of any way to create a pqr file of a ligand that is
> represented by the GAFF?

Use LEaP to create a prmtop file of the ligand, and then ambpdb with the -pqr
flag to create the pqr file.

Currently, it looks like antechamber can read pqr files but not write them.
Maybe this functionality can be added.

CAVEAT: The "ambpdb -pqr" program will transfer the charges from a gaff file
into the appropriate place in the pqr file. But gaff doesn't know anything
about dielectric radii. Ambpdb hard-codes these to Bondi radii. Check the
code to see what it is doing, or to change its behavior.

....dac
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