I see- well in the case that the original poster asked about (rotation of
backbone dihedrals in a monomer) it worked fine for me. there may be
problems in more complicated cases like yours.
On 3/5/07, Piotr Cieplak <cieplak.cgl.ucsf.edu> wrote:
>
>
> Yes, I wrote about that problem aroun the middle of last year.
> The problem occured to me when I tried to rotate a little bit a single
> -SG-HG group in CYS. It does not matter how I defined the order of
> rotation - e.g. UP or DOWN the tree the coordinates of the entire
> protein changed their position in space. And I wanted to keep the protein
> at the same place in space but just rotate a little bit one dihedral
> angle, as was possible with old EDIT program. The problem is more severe
> (as in my case) when one has let's say a protein dimer. After attempting
> to rotate single dihedral in one monomer the geometry of the entire
> complex is
> destroyed, because the monomer, where the bond rotation is attempted, is
> moved out of its place in space. I don't understand what kind of procedure
> is used for this type of simple transformation? It is difficult to read
> and understand leap for me.
>
> The original stuff I posted last year is in attachment.
>
> Best
> Piotr
>
>
> On Mon, 5 Mar 2007, M. L. Dodson wrote:
>
> > Date: Mon, 5 Mar 2007 11:42:13 -0600
> > From: M. L. Dodson <mldodson.houston.rr.com>
> > Reply-To: amber.scripps.edu
> > To: amber.scripps.edu
> > Subject: Re: AMBER: psi , phi angles
> >
> > 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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> >>
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> >
> > --
> > M. L. Dodson
> > Email: mldodson-at-houston-dot-rr-dot-com
> > Phone: eight_three_two-56_three-386_one
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
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> >
>
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Received on Wed Mar 07 2007 - 06:07:27 PST
