AMBER Archive (2008)

Subject: AMBER: How to set a ZN atom radius for PB calculations

From: Sam Danziger (
Date: Tue May 20 2008 - 19:23:30 CDT

I'm trying to use sander in Amber 10 to create a spacial distribution
of electrostatic potential however I run into the following error:

 SA Bomb in phi_aaradi(): No radius assigned for atom 1307 ZN

I know form this thread
( that if I turn the
gb off, then I should be able to proceed, however if I do that sander
seems to ignore the phiout=1 flag as I do not get the pbsa.phi file.

Two questions:
1) How do I use leap to set the atom radius for ZN? The documentation
implies that these radii should be included in the prmtop file.
2) Where is the pbsa.phi file when I set igb=0?

I'm using the following input file:

Sample PB visualization input
ntx=1, irest=0, cut=12,
imin=1, ntmin=2, maxcyc=0,
ntpr=1, igb=10, ntb=0,
ntc=1, ntf=1,
npbverb=1, istrng=0, epsout=80.0, epsin=1.0,
space=1., accept=0.0001, dbfopt=1,
sprob=1.4, cutnb=0, npopt=0,
phiout=1, phiform=1, radiopt=0

Thank you!

Samuel A. Danziger
Dept. of Biomedical Engineering
PhD Candidate
University of California
Irvine, CA 92697

Associated Graduate Students VP Financial Affairs

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