Hi Xing,
If you are trying to separate a protein apart then you can try SMD.
with regards,
-Abhishek
________________________________
From: Xing <stecue.gmail.com>
Sent: Wednesday, July 19, 2017 1:07:57 PM
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 Wed Jul 19 2017 - 18:00:03 PDT
