Dear, Amber users
I have equilibrated a box of 216 acetone molecules and I want to
solvate my host molecule with this box. However I have large problem
getting the entire host molecule solvated.
First I create an off-file for my solvated acetone box by the
following leap commands:
source leaprc.ff99SB
loadamberprep ace.in
ACEBOX = loadpdb acetone_equil_box.pdb
setbox ACEBOX vdw
saveoff ACEBOX ACEBOX.off
And then in another leap run I do the following commands:
source leaprc.ff99SB
loadamberprep ace.in
loadamberprep host.in
loadoff ACEBOX.off
x=loadpdb host.pdb
solvateoct x ACEBOX 15
And then I get a few acetone molecules in the corners of the
octahedralbox, but no solvent molecules any close to the host.
Best regards,
Samuel Genheden
University of Lund
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Received on Fri Apr 29 2011 - 05:30:08 PDT
