If you don't have a structure for the complex, I would suggest not starting
with Amber. There are good tools designed to do this, like Cluspro.
On Fri, Mar 22, 2024, 8:44 AM Matthew Guberman-Pfeffer via AMBER <
amber.ambermd.org> wrote:
> Dear AMBER Community,
>
> Background: I want to generate possible configurations for a homodimeric
> complex of a ~100-residue, well-structured protein. My interest is in
> evaluating the inter-protein electron transfer rate within the
> configurations for the complex.
>
> Question: I’d greatly appreciate suggestions on how to generate an
> ensemble of likely complexes? Is rigid-body Brownian dynamics possible in
> AMBER? Should I use protein-protein Gaussian Accelerated MD? etc.
>
> Best,
> Matthew
>
>
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Received on Fri Mar 22 2024 - 06:00:03 PDT
