On Tue, Jan 15, 2008, rdauria.uci.edu wrote:
>
> I need to set up a small system with ~80 water molecules and few ions,
> therefore I have solvated 4 simple ions (2 sodium and 2 chloride) in a
> POL3 water box with the command solvatedBox. I created with tleap the
> parm7, the coordinate file and also the pdb file with savepdb command. I
> used setBox to set the PDB. My final box is a 16 Angs cube. I have set the
> cutoff to 6. Angs.
I can't help with the specific problem, but Amber can't handle such small
systems very well. Basically, the box size must be at least twice (cut +
skinnb). Given than an 8 Ang. cutoff is a practical minimum with the current
codes, you are stuck with using larger systems.
You should also indicate exactly how you created the system, since that is
probably related to the actual error. There should be no need to use a setBox
command if you also used solvateBox, and I suspect that the origin of your
problem lies in that direction. But we need more details to provide help.
[Generally, to everyone: don't just say things like "I used setBox to set the
pdb". Please give the *exact* sequence of commands. Generally, when things
go wrong, it's because of details.]
...dac
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Received on Sun Jan 20 2008 - 06:07:07 PST
