AMBER Archive (2006)

Subject: Re: AMBER: pqr file

From: David A. Case (
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.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to