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
>
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Received on Wed Mar 07 2007 - 06:07:26 PST
