AMBER Archive (2009)

Subject: [AMBER] protein monomerizartion times and simulation with implicit solvent

From: drugdesign (
Date: Wed Feb 18 2009 - 04:27:17 CST

Dear Amber users,
I have a homology based model for homodimeric protein. For the template homodimer the native dimeric state is known and for modelled protein native monomeric state is known.
I've made a 2 nanosecod GB run for the modelled homodimeric protein but there seems to be no significant monomerization.
Maybe I need to use longer simulation periods with explicit water models to get monomerization? What times and conditions do you suggest?
Each monomer is about 120 amino acids.

Best regards,

AMBER mailing list