AMBER Archive (2002)

Subject: Re: restrain a residue as center of mass

From: eric hu (erichu_linux_at_yahoo.com)
Date: Wed Nov 27 2002 - 12:42:36 CST

Target md seems to satisfy what I want if I can use
zero RMSD. I really do not want any internal motions.
However, sander seems to stop running at a point. It
gives the same result no matter if I assign the
tgtrmsd or not.

   4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------

     eedmeth=4: Setting switch to one everywhere

 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 462
| TOTAL SIZE OF NONBOND LIST = 462
 SMALL DET 2.16840434497101D-019
 PROBLEM CALCULATING RMSDVALUE F

 Here is my input file.

 &cntrl
   igb = 0, ntb = 0, ntpr = 100, ntwx = 10,
   cut = 10.0,
   tempi = 300.0, temp0 = 300.0, ntt = 1, tautp = 0.5,
   imin = 0,
   nstlim = 1000, dt = 0.001,
   itgtmd=1
 &end
Restrain the residue
RES 1
END
END

--- Carlos Simmerling <carlos_at_csb.sunysb.edu> wrote:
> if you're using amber version 7, you could use
> targeted
> MD to do this. Check the manual, it is the itgtmd=1
> option in sander. What you want to do is to select
> using the
> GROUP input the residue to restrain, and then make
> sure
> to provide the reference coordinates for that
> residue. This
> will allow the residue to move as a group but will
> restrain
> it to be similar to the reference conformation. You
> will want
> to use a target rmsd value of something close to 0.
> Post again if this isn't what you want or doesn't
> work.
> Carlos
>
> ----- Original Message -----
> From: "eric hu" <erichu_linux_at_yahoo.com>
> To: <amber_at_heimdal.compchem.ucsf.edu>
> Sent: Tuesday, November 26, 2002 6:36 PM
> Subject: restrain a residue as center of mass
>
>
> > Hi, I want to freeze the internal motion of an
> > unnatural residue which happens to have two
> molecules.
> > I still want the residue's center of mass to have
> all
> > the freedoms. I wonder if there is way to do this.
> I
> > have tried to constrain individual atoms or bond
> > distances and they will either fix the atoms in
> the
> > space of there are still internal motions. Thanks
> a
> > lot.
> >
> > Regards,
> > -Eric
> >
> > __________________________________________________
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>

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