AMBER Archive (2005)

Subject: AMBER: The error during calculating PB with pbsa

From: zhli_2000_at_126.com
Date: Sun Dec 04 2005 - 22:39:19 CST


Dear all,
      When calculating the PB with pbsa, the error message is given in the
ligand outfile (pbsa_lig.1.out) as following:

 ======== Setting up Grid Parameters ========
 Using bounding box for grid setup
 Bounding Box Center: 31.164 48.892 40.586
 Xmin, Xmax, Xmax-Xmin: 25.292 37.036 11.744
 Ymin, Ymax, Ymax-Ymin: 42.157 55.627 13.470
 Zmin, Zmax, Zmax-Zmin: 36.134 45.039 8.905
   beginning box center at level 1 31.164 48.892 40.586
   beginning box center at level 2 31.164 48.892 40.586
 Grid dimension at level 1 7 9 5
 Grid origin corrected at level 1 15.164 28.892 28.586
 Grid dimension at level 2 39 43 35
 Grid origin corrected at level 2 21.164 37.892 31.586
PB Bomb in setgrd(): focusing grid too large 2
reset fillratio to a larger number 2.000

    I use the VMD to load the ligand, the first three structures of this
ligand are good. So I don't know how to deal with this problem.
      Please give me some advices. Thanks a lot!

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