> I used AmberTools 1.2 / tleap to generate this some time ago. But also
> tried using 1.5 recently. It behaved the same. The topology file is
> too big to send by email (this is a big system). Instead, I attached a
> figure to show what is going on. Red dots are waters. Cyan and blue
> balls are ions.
Clearly the ion distribution is not good/reasonable. What I do to get
around this behavior, albeit it slower, is to add fewer ions at a time...
> The input for tleap as follows:
>
> source leaprc.ff03
> source leaprc.GLYCAM_06
> X = loadpdb 3ije_mod.pdb
> solvateBox X TIP3PBOX 15
> addIons X Na+ 241 Cl- 203
addIons X Na+ 0
addIons X Na+ 5 Cl- 5
addIons X Na+ 5 Cl- 5
addIons X Na+ 5 Cl- 5
addIons X Na+ 5 Cl- 5
...
Best behavior is if 1 atom is added at a time...
addIons X Na+ 1 Cl- 1
(which you would do 203 times).
--tec3
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Received on Fri Jul 22 2011 - 13:00:02 PDT
