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
1PLC.inpcrd.pdb
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?
Thanks,
ThuZar
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Received on Wed Jul 06 2005 - 22:53:00 PDT
