AMBER Archive (2009)

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

From: Carlos Simmerling (
Date: Wed Feb 18 2009 - 06:16:00 CST

I think you need to look at the literature about things like this- we
can help with technical issues, but you really need to know what, if
anything, others have done before you try something extremely
challenging like this. monomer-dimer equilibrium is likely well beyond
the timescale of 2ns, or even 2 microsec. for any new project I
strongly encourage you to read the literature and see if it has ever
been done before, and if yes you can use that work as a guide. if no,
expect lots of trial and error as you go forward. as you run into
technical problems, ask about them here. it won't substitute, though,
for needing a thorough literature search first.

On Wed, Feb 18, 2009 at 5:27 AM, drugdesign <> wrote:
> 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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