On Mon, Jan 26, 2009, oguz gurbulak wrote:
> I'm now on Windows so I can only use rar or zip format for
> compressing files.
This is hardly true....just Google for "gzip windows" for example.
> the mail. I used packmol in order to get my pdb file that includes 100
> n-dodecane molecules. I added TER cards between each seperate n-dodecane
> molecule with using a script. You can examine my packmol pdb file attached
> to the mail.
You need to use the "set" command in LEaP to add the box information
after you load the packmol pdb file.
Also note: a box size of 9 Ang or so is too small for Amber. The box
size has to be at least twice the cutoff, so as a practical matter, the
smallest box that really works is about 18 Ang.
...dac
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Received on Fri Jan 30 2009 - 01:15:43 PST
