AMBER Archive (2009)

Subject: Re: [AMBER] Protein Domain Motion

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Aug 14 2009 - 07:17:28 CDT

domain motion tends to be slow, and you might need a lot of simulation to
get reliable data. it's possible, but challenging. as usual, I recommend
looking in the peer-reviewed literature for examples that are similar to
what you want to do and following their work. for projects where there is no
precedent in the literature, you should expect it to be very challenging,
especially if you don't have much experience with MD.

On Thu, Aug 13, 2009 at 9:51 PM, Chih-Ying Lin <chihying_at_usc.edu> wrote:

>
>
> Hi
> I am working on protein-ligand interaction and wander know the protein
> domain motion with existence of the ligand.
>
> Is it very challenging to simulate the Protein Domain Motion with MD?
>
> Thank you
> Lin
>
>
>
>
>
> ----- Original Message -----
> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> Date: Thursday, August 13, 2009 12:40 pm
> Subject: Re: [AMBER] Protein Domain Motion
> To: AMBER Mailing List <amber_at_ambermd.org>
>
> > yes it is possible- but probably challenging. impossible to say
> > more without
> > knowing what you want to do.
> >
> >
> > On Thu, Aug 13, 2009 at 3:20 PM, Chih-Ying Lin <chihying_at_usc.edu>
> > wrote:
> > >
> > >
> > >
> > >
> > >
> > > Hi
> > > Is it possible to simulate the Protein Domain Motion by MD ?
> > >
> > >
> > > Thank you
> > > Lin
> > >
> > >
> > >
> > >
> > >
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