Re: AMBER: pbsa error in mm_pbsa amber 8

From: Ben Cossins <>
Date: Thu, 9 Dec 2004 15:19:20 +0000

Hey again,
  Sorry I should have said that the calculation does not fail but the ligand
solvation energies fluctuate enourmousely and have SD's of around 1900.


On Thursday 09 Dec 2004 14:58, Ben Cossins wrote:
> Hey,
> I have been using mm_p-bsa from amber 8 to calculate binding energies of
> ligand-receptor systems. I get an error from pbsa when it is calculating
> ligand solvation energy for some ligands and not for others.
> The message is:-
> PB Warning in epsbnd(): No neighbor found for reentry boundary grid
> I have applied all bug fixes.
> I have had a look at the code giving this error but dont instantly see what
> the error is for. I have seen that there has been a bug fix (bug fix4) a
> few lines above this.
> Can anyone offer me any advice.
> Thanks
> Ben

Benjamin Cossins
Southampton University
J. W. Essex group.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Dec 09 2004 - 15:53:00 PST
Custom Search