AMBER Archive (2007)

Subject: Re: AMBER: psi , phi angles

From: Piotr Cieplak (cieplak_at_cgl.ucsf.edu)
Date: Mon Mar 05 2007 - 13:27:13 CST

Unfortunately my case belongs also to "a simple" one as well.
Even when trying to change that simple C-C-SG-HG dihedral in a monomer
the entire protein changes its position in space. I don't want this
type of behavior, because it creates many other problems further on (with
setup, especially in water, with analysis, referencing to some other
structures etc...).
So, instead of x/tleap I am forced to use some external graphics programs,
which impedes the setup process and makes any eventual pipelining a
nightmare. Of course, the solution is to write my own simple program.

P.

On Mon, 5 Mar 2007, Carlos Simmerling wrote:

> Date: Mon, 5 Mar 2007 13:56:46 -0500
> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> Reply-To: amber_at_scripps.edu
> To: amber_at_scripps.edu
> Subject: Re: AMBER: psi , phi angles
>
> 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_at_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_at_houston.rr.com>
>> > Reply-To: amber_at_scripps.edu
>> > To: amber_at_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_at_gmail.com>
>> >>> Reply-To: amber_at_scripps.edu
>> >>> To: amber_at_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_at_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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>> >
>>
>
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