Dear Amber users!
I've performed some equilibration simulation of my water-soluble protein
having internal cavity permeable for the solvent water. Foe the trajectory
analysis I've noticed that several water have been moved inside the protein
and made hydrogen bonds with the polar side chains. Now I've selected my
protein with these internal waters in the separate pdb and would like to
resolvate this system and perform new simulation. My questions.
1) Does it possible to keep internal water within my protein with this new
model? How I should define internal water (as the ligand for instance )?
2) More general question. What model for solvent water should be used
better for modelling permeation of the solvent within protein?
TFH,
James
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Received on Wed May 21 2014 - 06:00:04 PDT
