Dear amber users，
I want to calculate the binding free energy between two domains of a kinase. The domains own 264 and 222 residues respectively. While I calculate with PBSA, however, it reports a "PB bomb" error. The error message is "Number of SA srf points exposed 65233
PB bomb in pb_saarc(): Allocation aborted 0, 2*4205". Which parameter should I modify to fix the problem? Thanks!
The files mm_pbsa.in and the final part of pbsa_com.1.out are listed below.
mm_pbsa.in.
################################################################################
.GENERAL
PREFIX kd_pbd
PATH ../1_Snapshots/
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../kd_pbd.top
RECPT ../kd.top
LIGPT ../pbd.top
#
GC 0
AS 0
DC 0
#
MM 1
GB 0
PB 1
MS 1
#
NM 0
################################################################################
.PB
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2.0
LINIT 500
PRBRAD 1.6
#
RADIOPT 1
#
FOCUS 0
PERFIL 80.0
CHARGE ../my_amber94_delphi.crg
SIZE ../my_parse_delphi.siz
#
SURFTEN 0.005
SURFOFF 0.0
#
################################################################################
.MM
DIELC 1.0
#
################################################################################
.GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
.MS
PROBE 0
#
#################################################################################
.PROGRAMS
DELPHI /user_data2/accelrys/I2005/irix6m4/biosym_exe/delphi
SANDER /userdata/zgliu/program/amber8/exe/sander
#
################################################################################
output of pbsa:
################################################################################
4. RESULTS
--------------------------------------------------------------------------------
NB-update: residue-based nb list 3501439
NB-update: atom-based nb list 872381
======== Setting up Grid Parameters ========
Using bounding box for grid setup
Bounding Box Center: 46.585 42.917 46.743
Xmin, Xmax, Xmax-Xmin: 9.709 83.462 73.753
Ymin, Ymax, Ymax-Ymin: 8.908 76.926 68.018
Zmin, Zmax, Zmax-Zmin: 7.882 85.603 77.721
beginning box center at level 1 46.585 42.917 46.743
beginning box center at level 2 46.585 42.917 46.743
Grid dimension at level 1 37 35 41
Grid origin corrected at level 1 -29.415 -29.083 -37.257
Grid dimension at level 2 165 153 171
Grid origin corrected at level 2 5.085 4.417 3.743
Number of SA srf points exposed 65233
PB bomb in pb_saarc(): Allocation aborted 0, 2*4205
=========================================================================================
Best regard!
zgleo
2005-11-22
___________________________________________
Zhiguo Liu
Ph.D candidate
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
Chinese Academy of Science
Shanghai, China
zhiguo.leo.gmail.com
zgliu.sibs.ac.cn
___________________________________________
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Received on Tue Nov 22 2005 - 02:53:00 PST
