Hi,
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.
Is there any thing else which I need to take care?
Thanks,
Hirdesh
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Received on Thu Sep 29 2016 - 05:00:02 PDT
