On Thu, Sep 29, 2016, Hirdesh Kumar wrote:
>
> I have a protein-ligand complex in truncated octahedran box. I did minor
> modifications (deleted two atoms) in the system and want to start a new
> simulation using the old waterbox information.
>
> I tried to use setbox as follows:
> set var box {85.030 85.030 85.030}
>
> however, when i started the new simulation, I found the waterbox changed
> into "square" .
>
> then I changed IFBOX pointer in the prmtop file from 1--> 2.
>
> Now the trajectory looks fine.
Check the final line of the rst7 file from the new calculation: is it the same
as the final line from the earlier simulation? If so, you are probably in
good shape. If not, there are probably problems.
....good luck....dac
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Received on Thu Sep 29 2016 - 12:30:03 PDT
