AMBER: problem with addIons

From: Lwin, ThuZar <>
Date: Wed, 6 Jul 2005 16:41:25 -0500

Dear Amber users,

    My protein has a negative charge of -8. When I neutralize this system as
addIons protein Na+ 0
all the sodium ions are added to one corner of the solvation box. I tried it on different machines, and it still does the same behaviour.
    Lastly, I downloaded the pdb file from amber8 tutorial
this pdb also shows ions at one corner.
    Isn't counter ions supposed to be scattered and appear near the charged residues like they appear in DNA? Why isn't addIons working for the case of proteins? Or am I doing something wrong?


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jul 06 2005 - 22:53:00 PDT
Custom Search