[Chimera-users] Solvate Tool Trouble

Mike Bergman bergm310 at umn.edu
Wed Jul 20 11:42:13 PDT 2016

Hey there.
I am having trouble with the solvate tool. I am using a dimeric model
(PDB ID: 2Q1E) that isn't attached. Every time I try to solvate (model
TIP3PBOX), it squishes the dimer together. I tried different angstrom
box sizes - 3, 5, 10, 20. Running the simulation with them overlaid
wouldn't give me any useful data as I'm looking for the changes in the
dimer interface.
Is there a way I can stop it from doing this? Should I use a different
solvate method like Shell?
Mikey Bergman

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