Dear Amber users!
I am focusing on the protein-membrane tutorial using the pacmol-memgen
utility. The protein embedded into the lipids consist of both large
transmembrane domain as well as large disordered segment exposed to
water from one side of the membrane (not embedded into the membrane)
I have a question about added solvent.
In the case if I specify explicitly the XY dimensions of the membrane
by means of the --distxy_fix , the disordered segment of the protein
(not embedded into the membrane) remains not fully covered with water
(also some water was added in both leaflets).
If I additionally specify the size of the water layer via --dist_wat,
it adds symmetrically the water layer from both sides of the membrane
so the disordered fragment is fully covered. However I do have a big
water layer from the other side of the membrane, which is not required
for my system.
Could I specify via some combination of the options the width of the
water layer only in contact with the protein atoms ? Otherwise, would
it be OK to start simulation from the system with not fully exposed to
the solvent segment which normally should be treated correctly via PBC
?
Many thanks in advance
Yours with thanks
Enrico
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Received on Thu Aug 31 2023 - 06:30:02 PDT
