Emilia,
Since you are using gaff force field, as indicated by lower-case atom types,
please set radiopt = 0 to use the radii in your prmtop file.
Best,
Ray
==========================================
Ray Luo, Ph.D.
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900
Phone: (949) 824-9528
Email: rluo.uci.edu
Web: http://rayl0.bio.uci.edu/
==========================================
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
emilia wu
Sent: Friday, January 19, 2007 5:16 AM
To: amber
Subject: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3
f
Dear amber users,
I try to calculate the binding free energy of an inhibitor and a protein
with MM/PBSA using Amber9,
but it stopped and the output tell me that"PB Bomb in pb_aaradi(): No radius
assigned for atom
4474 F3 f". and there is a fluorin atom in the inhibitor, so how to fix
it, if I should add some
radius parameters for fluorin, which file should be modified, and what
parameter should I use?
thanks in advance!
emilia wu
emiliawu.dicp.ac.cn
2007-01-19
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Received on Sun Jan 21 2007 - 06:07:41 PST
