Thanks, treat suggestion! But my protein has a heme cofactor. For the docking stage with Cluspro, then, do I have to pretend that the heme is not present and then add it back to each protein in the docked configuration? (The heme is mostly buried, but the propionic acid substituents may contribute to the interface.)
Best,
MAtthew
> On Mar 22, 2024, at 8:53 AM, Carlos Simmerling <carlos.simmerling.stonybrook.edu> wrote:
>
>
> *Message sent from a system outside of UConn.*
>
>
> 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 <mailto: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 - 07:00:02 PDT
