Dear amber users,
Did anyone found this similar problem ? I got some errer after performed
mm-pbsa for calculating the binding free energy. The error shown some
mistake in trajectories 2 as follows:
/AMBER/amber9/exe/pbsa -O -i pbsa.in -o pbsa_com.2.out -c
../01_generate_snapshot/snapshot_com.crd.2 -p ./enz-lig.top not successful
When i check the output file of pbsa_com.2.out which you can see below. It
seems like the problem from setting grid. And the output of the
snapshot_com.all.out stop at trajectories no.2 which indicate some unknown
parameters or the maximum of somethings.
So, anyone who had been experienced for this problem like me, please give me
some suggestions to solve. That would be grate for me.
pbsa_com.2.out
======== Setting up Grid Parameters ========
Using bounding box for grid setup
Bounding Box Center: 3.500 -5.500 25.500
Xmin, Xmax, Xmax-Xmin: -157.543 164.986 322.529
Ymin, Ymax, Ymax-Ymin: -175.901 165.219 341.120
Zmin, Zmax, Zmax-Zmin: -154.928 205.819 360.747
beginning box center at level 1 3.500 -5.500 25.500
beginning box center at level 2 3.500 -5.500 25.500
Grid dimension at level 1 163 173 181
Grid origin corrected at level 1 -324.500 -353.500 -338.500
Grid dimension at level 2 659 697 735
Grid origin corrected at level 2 -161.500 -180.000 -158.500
PB bomb in pb_setgrd(): Allocation aborted 41 41
41
41 179 0 41 0 0
0 0 0 0 41 0
0 41 41 41 41 41
41 41 41 41 41 0
0 0 0
snapshot_com.all.out
MM
GB
PB
MS
1
BOND = 706.9730 ANGLE = 1873.4731 DIHED =
2204.7529
VDWAALS = -1630.5701 EEL = -13788.9361 EGB = -
4298.7432
1-4 VDW = 771.1222 1-4 EEL = 7509.8232 RESTRAINT =
0.0000
corrected reaction field energy: -7009.180494
surface area = 11616.363
ECAVITY = 11616.363
EDISPER = 0.0000
2
BOND = ************* ANGLE = 344577.8827 DIHED =
10792.3243
VDWAALS = NaN EEL = Infinity EGB = -
19816.9010
1-4 VDW = NaN 1-4 EEL = Infinity RESTRAINT =
0.0000
Thanks,
Jitrayut
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Received on Wed May 02 2007 - 06:07:06 PDT
