Minimization problem w/ counter-ion !

From: Marco Preto <>
Date: Thu, 31 Oct 2002 02:54:27 +0000

Dear Amber users:

I'm trying to run a minimization of a solvent box (with my solute and
Cl- fixed) to get a better starting point to the equilibration dynamic
run of my system. Unfortunatly I'm having trouble with the electrostatic
interactions (this value goes to so negative magnitude that the format
is not suficient to writ it and my output comes like ***********. I've
tryed to put the counter ion using addions and when that did not work I
tryed to put it manually on my system, in diferent positions, but the
calculations allways stoped with a segmentation fault, during this
I guess the problem is with the counter ion because I have been running
the same protocol on non charged solutes and it runs without anyproblem
at all!
I'm using Amber6 and my solute is a small peptide (8 residues). Here is
the minimization input:

imin=1, maxcyc=200000, cut=12, igb=0,
ntb=1, ntpr=1000, ncyc=2000,
ibelly=1, ntwx=100,
Group input for moving atoms
RES 10 3846

Res 10 to 3846 are my water molecules! I know that running Ewald and
belly simultaniously is not correct but that's not the reason why the
calculation is dieing!

Can anyone bring some light to this problem?

Sincerely yours

 Marco A. C. Preto               |"Quantum temporis lucratur qui non
 PH.D. student                   |aspicit quod vicinus dicit, agit
 Theoretical Chemistry group     |vel cogitat, sed tantum quod ipse
 Chemistry Deparmant - FCUP      |agit ad id iustum et sanctum 
 Porto, Portugal                 |reddendum"
                                 |   from my homonimous
email:          |  
                                 |                 Marcus Aurelius
Received on Thu May 22 2003 - 17:53:01 PDT
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