On Thu, Jan 19, 2012, Jorgen Simonsen wrote:
> sure - sorry for the lack of information. So I ran the minimization
> without periodic boundary condition and it work - so during the
> generation of prmtop/inpcrd without adding any water to the system
> also no boundary conditions were added - so my solution would be to
> copy the pbe from the first prmtop/inpcrd and use that - from the
> manual it looks like it is the last line in the inpcrd file so paste
> it into the new inpcrd file would that solve the problem?
Better to use the "set" command in leap to add the box, e.g. (roughly!)
x = loadpdb <modified pdb file with a specific number of waters>
set x box { 31.2 34.2 29.8 } <= numbers are the lengths of the sides
of the box
saveamberparm x prmtop.new incprd.new
See if that helps...note that both the prmtop file and the inpcrd file will
have information that relates to the box.
...dac
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Received on Thu Jan 19 2012 - 06:30:03 PST
