Hi all,
I am trying to calculate the binding enthalpy of protein-ligand system
using explicit solvent.when I followed the Amber tutorial 21, they have
mentioned that the water molecules should balance between the bound set of
simulations(complex and pure water) and unbound set of simulatuions(host
and guest).How can I add equal number of water molecules between the bound
and unbound set of simulations?What could be the proper box size for the
leap preparatory files.In amber tutorial 21, they have used following box
sizes for bound and unbound states.
solvatebox purewater TIP3PBOX 16.50 iso
solvatebox b2 TIP3PBOX 13.16 iso
solvatebox CB7 TIP3PBOX 10.18 iso
solvatebox b2-CB7 TIP3PBOX 9.91 iso
They have also removed water above 1500 to maintain equal number of water
molecules between bound and unbound set of simulations.
Thanking you in advance,
Dipesh,
graduate student,Idaho Satte university
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 03 2016 - 10:30:04 PDT
