AMBER Archive (2009)

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

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Fri Dec 04 2009 - 11:09:17 CST

> 1) When Na+ is added before solvation 3686 H2O molecules are added (Box X =
> 51.627 Box Y = 58.077 Box Z = 56.547)

The "Na+" is being considered as part of the solute so the resulting box
will be bigger. Also, depending on your system, you may be better off
with a truncated octahedron (solvateOct in LEaP) since this will be
smaller (or similarly sized ) but more symmetric (i.e. rotation of the
solute will not lead to closer approach of periodic images).

> 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

"SOD" happens to be the name of sodium residues in CHARMM; every force
field in principle could have its own name. In older AMBER, this was "NA"
or "IP" and in newer force fields the residue name is "Na+".

-- tec3

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