AMBER Archive (2009)

Subject: RE: [AMBER] fillratio error in mmpbsa

From: Ray Luo (rayhuangluo_at_gmail.com)
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

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf
Of m m
Sent: Wednesday, April 01, 2009 4:43 AM
To: amber_at_ambermd.org
Subject: [AMBER] fillratio error in mmpbsa

Hi,

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 pbsa_lig.in -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
2.000
when i add fillratio=4 to pbsa_lig.in, ans i do just: sander -O -i
pbsa_lig.in -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?
Thanks

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