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
(
http://amber.ch.ic.ac.uk/archive/200701/0253.html) 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
&cntrl
ntx=1, irest=0, cut=12,
imin=1, ntmin=2, maxcyc=0,
ntpr=1, igb=10, ntb=0,
ntc=1, ntf=1,
/
&pb
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!
-Sam
--
Samuel A. Danziger
Dept. of Biomedical Engineering
PhD Candidate
University of California
Irvine, CA 92697
sdanzige.uci.edu
(908)246-4502
http://samdanziger.com/
Associated Graduate Students
VP Financial Affairs
vpfinance.ags.uci.edu
Truth Cannot Contradict Truth
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Received on Wed May 21 2008 - 06:07:54 PDT
