AMBER Archive (2009)

Subject: RE: [AMBER] fillratio error in mmpbsa

From: Ray Luo (
Date: Wed Apr 01 2009 - 14:24:20 CDT

Could you be more specific? What is the error message in the output file
after setting fillratio to 4?

All the best,

Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email:
Phones: (949) 824-9528, 9562

-----Original Message-----
From: [] On Behalf
Of m m
Sent: Wednesday, April 01, 2009 4:43 AM
Subject: [AMBER] fillratio error in mmpbsa


i run mmpbsa calculation with amber10, i have no probleme with extrat
coordodinate, but with binding energy
 the calculation stop with this message error:
sander -O -i -o pbsa_lig.155.out -c ./snapshot_lig.crd.155 -p
./mmR18.prmtp not successful
In pbsa_lig.155.out i found: PB Bomb in setgrd(): focusing grid too
large 2
                                         reset fillratio to a larger number
when i add fillratio=4 to, ans i do just: sander -O -i -o pbsa_lig.155.out -c ./snapshot_lig.crd.155 -p ./mmR18.prmtp
not successful, i obtain a good pbsa_lig.155.out.
what can i do to resolve this problem?

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