that sounds reasonable, but this isn't really my area of expertise. you
might try contacting the cluspro developers midas.laufercenter.org
On Fri, Mar 22, 2024 at 9:54 AM Matthew Guberman-Pfeffer <
matthew.guberman-pfeffer.uconn.edu> wrote:
> 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> 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 Mon Mar 25 2024 - 06:30:02 PDT
