HI,
Not different conformations but slowly pulling apart the dimer by adding restrain potentials to direct them to move away.
Alternatively, like someone else on the list suggested you can also use SMD.
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: Xing <stecue.gmail.com>
Sent: 20 July 2017 05:37
To: amber.ambermd.org
Subject: Re: [AMBER] pull a dimer apart in AMBER?
Dear Elvis,
Sorry I just saw the reply. Thanks! Do you mean that I can set up a series of different starting conformation in which the distance between the dimer is different and see how stable those
conformations are?
Thanks and best wishes,
Xing
On 07/04/2017 11:52 PM, Elvis Martis wrote:
> HI,
> Seems possible. You can try umbrella sampling.
> DOI: 10.1002/wcms.66 this is the reference.
>
> Best Regards
> Elvis Martis
> Mumbai, INDIA.
>
> ________________________________________
> From: Xing <stecue.gmail.com>
> Sent: 05 July 2017 07:54:12
> To: AMBER Mailing List
> Subject: [AMBER] pull a dimer apart in AMBER?
>
> Dear Amber users,
>
> I'm trying to "pull" a protein dimer apart in MD, or at least trying to
> see if the dimer is still stable by applying a pair of force to a
> certain pair of amino acid residues. Can I do that in AMBER or is there
> any published literature about that?
>
>
> Thanks and best wishes,
>
> Xing
>
>
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Received on Thu Jul 20 2017 - 03:30:02 PDT
