AMBER Archive (2009)

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

From: drugdesign (drugdesign_at_yandex.ru)
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,
Andrew

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