On Mon, Sep 20, 2010, xue wang wrote:
>
> I finally identified the origin of the problem: in "leap.in", I set "set
> default pbradii bondi" which indicates implicit solvent, and I solvate
> protein into water box, and in "min.in" I set "ntb = 1" which indicates
> periodic boundary. These commands are not consistent with each other.
I am glad things seem to be working for you, but I don't think the
explanation above is correct. Amber stores "PB" radii in the prmtop
file, even if they are not used, and nothing bad should happen if you use the
"set default pbradii" command. As best I can tell (and we may never
know), you tried to use ntb=1 on a prmtop file that was not set up for
periodic boundary conditions. As I mentioned before, I always get
an error message when this happens, and am not sure why that was not
happening for you.
....dac
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Received on Mon Sep 20 2010 - 18:30:05 PDT
