AMBER Archive (2007)

Subject: AMBER: MM-PBSA: Can't finish the binding energy process

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Mon Apr 23 2007 - 07:34:48 CDT

Dear amber users,

I have run the binding_energy.in in order to obtain the binding free energy
in term of COM, LIG, REC. The output name "snapshot_statistics.out" should
be generated but it stop at the process line below:

pbsa_lig.14.out

And, I also check the end of this file which its details show below:

 ======== Setting up Grid Parameters ========
 Using bounding box for grid setup
 Bounding Box Center: 43.000 33.500 40.000
 Xmin, Xmax, Xmax-Xmin: 34.354 51.926 17.572
 Ymin, Ymax, Ymax-Ymin: 20.466 46.695 26.229
 Zmin, Zmax, Zmax-Zmin: 35.378 44.181 8.803
   beginning box center at level 1 43.000 33.500 40.000
   beginning box center at level 2 43.000 33.500 40.000
 Grid dimension at level 1 11 15 5
 Grid origin corrected at level 1 19.000 1.500 28.000
 Grid dimension at level 2 49 67 33
 Grid origin corrected at level 2 30.500 16.500 31.500
PB Bomb in setgrd(): focusing grid too large 2
reset fillratio to a larger number 2.000

Actually, i perform the same protocal for other similar system and i can
obtain the output but why these errors
still occurs.

Therefore, anyone who can give me some suggestions would be appreciated.

Jitrayut Jitonnom

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