the NEB option in sander is probably the best Amber option for this.
You could also run targeted MD, starting with one structure and using
the RMSD restraint to force it to the other, but that can give high
forces at the start and tends to give direct paths that may not be
optimal.
If you go with NEB, use the Amber11 version. A tutorial and journal
reference for our NEB version can be found at
http://ambermd.org/tutorials/advanced/tutorial5_amber11/
On Tue, Apr 12, 2011 at 7:43 AM, Bernhard Poll
<poll.chemie.uni-hamburg.de> wrote:
> Hi Amber users,
>
>
>
> I've got some questition about MD's. Is it possible to define some start and
> end structure (and may be a transition state) of a protein in Amber and run
> a MD simulation? We know these points from crystal analysis and we're just
> wondering if it is possible to run the transition so we can understand this
> behavior.
>
>
>
> Thanks in advance
>
>
>
> Bernhard
>
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Received on Tue Apr 12 2011 - 05:00:04 PDT
