I'll look into this- it may be due to using
a target rmsd of zero. try a small non-zero value.
Carlos
----- Original Message -----
From: "eric hu" <erichu_linux_at_yahoo.com>
> 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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Received on Wed Nov 27 2002 - 13:38:57 PST
