Hi,
'solvatebox solute {a b c}' in tleap will apply 'a' for the x axis in
both +x and -x directions, and similarly 'b' for y and 'c' for z. I have
a protein that undergoes a huge conformational swing along, say, the z
axis. Furthermore I have reasons to restrain the protein in such a way
that the swing only occurs in the +z direction. Therefore I would like
to setup a box that extends significantly more in the +z direction than
it does in the -z direction. It seems that I cannot do that with
solvatebox. Is there a way to post process the box as well as the parm7
file to retroactively remove a slab of superfluous water from the box?
Thanks for your help,
Istvan
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Received on Sat May 04 2024 - 11:00:02 PDT
