AMBER Archive (2005)

Subject: AMBER: Question about PB bomb

From: zgleo (zgleo_at_tom.com)
Date: Mon Nov 21 2005 - 20:11:08 CST


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_at_gmail.com
zgliu_at_sibs.ac.cn
___________________________________________

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