[AMBER] protein monomerizartion times and simulation with implicit solvent

From: drugdesign <drugdesign.yandex.ru>
Date: Wed, 18 Feb 2009 13:27:17 +0300

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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Received on Fri Feb 20 2009 - 01:07:22 PST
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