On Monday 05 March 2007 11:29, Piotr Cieplak wrote:
> No, "impose" does not work correctly.
> P.
>
Well, I agree that my experience using "impose" is,
hmmmm.... interesting, but why do you say it does not work
correctly?
I would suggest the best approach to this is an umbrella sampling
protocol with sander. See page 158 of the amber9 manual. You
will need a 2D version of this example to sample both phi and psi.
Bud Dodson
> On Mon, 5 Mar 2007, Carlos Simmerling wrote:
> > Date: Mon, 5 Mar 2007 07:08:27 -0500
> > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > Reply-To: amber.scripps.edu
> > To: amber.scripps.edu
> > Subject: Re: AMBER: psi , phi angles
> >
> > check the manual, you can use the "impose" command
> >
> > On 3/5/07, deepti nayar <deepti.icgeb.gmail.com> wrote:
> >> hi
> >>
> >> I have build a phe-phe dipeptide using xleap. my next task is to
> >> change the torsion angles (psi and phi) at a certain interval and then
> >> note the corresponding energy. can anybody tell me if there is any way
> >> out to do it using leap (amber9).
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--
M. L. Dodson
Email: mldodson-at-houston-dot-rr-dot-com
Phone: eight_three_two-56_three-386_one
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Received on Wed Mar 07 2007 - 06:07:24 PST
