AMBER Archive (2005)

Subject: AMBER: warning in PBSA

From: Fabien Cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Wed Mar 23 2005 - 07:39:00 CST

Dear all,

I have problems when using PBSA program on my systems, when running
MMPBSA analysis.
I have a system of roughly 3300 atoms.
The calculations ends but there is one warning in the outuput file :
PB Warning in epsbnd(): No neighbor found for reentry boundary grid
What does this warning mean ?
The second problem is with a system with 6600 atoms.
The calculation stops with an error message in the output :
PB bomb in pb_saarc(): Allocation aborted

I am working on a Linux machine with 2G of physical memory.

The input file for PBSA is :
File generated by mm_pbsa.pl. Using PB
 &cntrl
  ntf = 1, ntb = 0,
  igb = 10, dielc = 1.0,
  cut = 99999.0, nsnb = 99999,
  scnb = 2.0, scee = 1.2,
  imin = 1, maxcyc = 0, ntmin = 2,
 &end
 &pb
  epsin = 1.0, epsout = 78.5,
  istrng = 0, radiopt = 0,
  sprob = 1.4, space = 2,
  maxitn = 250
  npbverb= 1
 &end

Thanks in advance for your answers,
Fabien 

-- 
__________________________________________________________________
Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail : cailliez_at_ibpc.fr
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
__________________________________________________________________

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