20 Jul
2016
20 Jul
'16
11:42 a.m.
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? Thanks. Sincerely, Mikey Bergman