AMBER Archive (2004)

Subject: AMBER: mm_pbsa problem

From: steven.j.enoch_at_gsk.com
Date: Fri Jul 02 2004 - 05:29:57 CDT

Dear AMBER users,

I am trying to perform mm_pbsa calculations on snapshots from a 300ps md
simulation carried out in explicit water with the pbsa module of AMBER 8 on
an SGI origin with the following set up:SGI 300 MHZ IP27 processors, CPU:
MIPS R12000 Processor Chip Revision 2.3, FPU: MIPS R12010 Floating point
chip revision 2.3, OS IRIX 6.5.20M.

The caluclation has no problems with the complex, or the receptor parts,
however when its tries to calculate the ligand contributions the program
crashes with the following error reported in the pbsa_lig.1.out file:

======== Setting up Grid Parameters ========
Using bounding box for grid setup
Bounding Box Center: 35.664 10.838 17.527
Xmin, Xmax, Xmax-Xmin: 31.182 40.146 8.964
Ymin, Ymax, Ymax-Ymin: 5.985 15.690 9.705
Zmin, Zmax, Zmax-Zmin: 11.489 23.565 12.076
beginning box center at level 1 35.664 10.838 17.527
beginning box center at level 2 35.664 10.838 17.527
Grid dimension at level 1 5 7 7
Grid origin corrected at level 1 23.664 -5.162 1.527
Grid dimension at level 2 35 35 41
Grid origin corrected at level 2 26.664 1.838 7.027
PB Bomb in setgrd(): focusing grid too large 2
reset fillratio to a larger number 2.000

I have tried running a gbsa simulation at that works fine, so I know the
parameter files are OK, interestingly sometimes the pbsa calc runs for
several ligand snapshots, with everythng looking fine and then it stops
with the same error.

Any help with this would be greatly appreciated - as its starting to drive
me crazy!!!

Thanks

Steve

Input file

@GENERAL
#
PREFIX 1_10
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../md_30ps_avd+btn.top
RECPT ../md_30ps_avd.top
LIGPT ../md_30ps_btn.top
#
#
GC 1
AS 0
DC 0
MM 1
GB 1
PB 1
MS 1
NM 0
#
#
@PB
#
PROC 2
REFE 0
INDI 1
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.6
RADIOPT 0
#
#
@GB
#
IGB 1
GBSA 1
SALTCON 0
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
#
#
@MM
#
DIELC 1.0
#
#
@MS
#
PROBE 0.0
#
#
@NM
#
DIELC 4
MAXCYC 10000
DRMS 0.0001
#
#
@MAKECRD
#
BOX No
NTOTAL 3460
NSTART 1
NSTOP 50
NFREQ 5
#
NUMBER_LIG_GROUPS 1
LSTART 1918
LSTOP 1948
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 1917
#
#
@TRAJECTORY
#
TRAJECTORY ../md_300ps.crd
#

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu