On Tue, Sep 28, 2010, subrata paul wrote:
> First we creat 10 disaccharide in xleap using GLYCAM_06 force field.
> then we
> >solvatebox 10_disa SPCBOX 3.0
^^^^^^
This is (probably) way too small a solvent shell. If you want to make a "box"
with a certain concentration of sugars in water, I suggest you look at the
packmol program.
> This is not a cubic box .
Correct; amber has no simple way to enforce a cubic box. I'm not sure if/how
packmol addresses this requirement.
> to make cubic box we set..
> > set 10_disa box {32.0 32.0 32.0}
This statement might be causing the problem; try first using a bigger water
shell, and avoiding this statement. That will give you some experience with a
non-cubic box. Then you can tackle the problem of how to make everything
cubic (assuming that is really needed).
...good luck....dac
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Received on Tue Sep 28 2010 - 09:00:09 PDT
