Re: AMBER: Restraint of atoms during minimization

From: Thomas E. Cheatham, III <>
Date: Tue, 22 Feb 2005 10:36:42 -0700 (Mountain Standard Time)

> It seems to me that the makeCHIR_RST command is used to generate dihedral
> restraint for amino acids only. But my molecule is a disaccharide. And I want
> to fix the two dihedral angles across the glycosidic linkages.

You can make your own list of restraints in the input file; see sections
two and three of the sander input (5.7 and 5.8) section of the AMBER8
manual, but basically a simple mdin would look like:

MD production
  imin = 1, maxcyc = 50000, drms = 0.0005, ntb = 0,
  ntpr = 100, cut = 999., ncyc = 1000, ntr=1,

  nmropt = 1,

   type ='END',

And if you wanted to restrain atoms C2, C3, C4, C5 in residue 9 to a
value of 180.0 degrees with a force constant of 5.0 the restraint like would look like:

 &rst iresid = 1, iat = 'C2', 'C3', 'C4', 'C5',
   r1 = 160, r2=180, r3 = 180, r4 = 200, rk2 = 5.0, rk3 = 5.0, &end

For more info, see the tutorials (like the DNA NMR one) but note that you
do not have to use those provided scripts to build the input; you can do
this by hand...

> Is there any other method to do this kind of minimization with restraint of
> dihedral angles for saccharide within AMBER? By the way, is it reasonable to
> use Cartesian coordinate restraints to restrain a dihedral angle?

Remember that these are restraints and not constraints (i.e. the values
are not fixed but will oscillate around the desired value with a
particular spring constant); cartesian restraining two dihedrals (if
separate) doesn't make sense since you will inhibit any independent motion
between the two dihedrals.

Good luck.

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Received on Tue Feb 22 2005 - 17:53:00 PST
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