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

From: Thomas Cheatham III <>
Date: Fri, 4 Dec 2009 10:09:17 -0700 (Mountain Standard Time)

> 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

AMBER mailing list
Received on Fri Dec 04 2009 - 09:30:03 PST
Custom Search