[AMBER] sodium ions before or after solvation makes a difference

From: Naser Alijabbari <na3m.virginia.edu>
Date: Fri, 4 Dec 2009 00:01:13 -0500

Hello, I am sorry if this has been asked before but I couldn't find a
response in the archives.
For an 8 angstrom of water shell around a protein I get 3500 H2O molecules
( Box X =51.627 Box Y =56.610 Box Z =56.547)
1) When Na+ is added before solvation 3686 H2O molecules are added (Box X =
  51.627 Box Y = 58.077 Box Z = 56.547)
2) When Na+ is added after solvation there are 3496 H2O molecules (which
makes sense) (Box X = 51.627 Box Y = 56.610 Box Z = 56.547)
What happens in case 1?
The second problem is that i can't see the Na+ in VMD for some reason. ambpdb
creates a pdb file with Na+ ions but using 'resname SOD' gives nothing in
VMD. Thanks
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Received on Thu Dec 03 2009 - 21:30:02 PST
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