Dear all,
I have a pdb file (and top/crd) of a system already solvated in an
truncated octahedral box. Now I apply a minor change in the system (pdb
file) to obtain a second system.
How do I proceed to setup a box from the modified pdb file with the same
dimensions but without resolvating the system, i.e. without using the
solvateoct command in leap?
The leap manual describes the "set box" command: Giving one additional
argument sets a cubic box, whereas giving a list of three numbers gives
the lengths of the sides in A.
Is the following approach sufficient where I obtain the length XXX from
the known system (crd file)?
# Leap script setting a known box dimension
a = loadpdb "a_oct_inp.pdb"
set a box XXX
saveamberparm a a.top a.crd
# End script
Any comment is welcome!
Best regards,
Anselm
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Received on Sun Apr 21 2013 - 09:30:03 PDT
