Restraints implies use of an energy function without absolute fixing of the desired quantity; the refc file can be used for restraining Cartesian coordinates of selected atoms, or internal coordinate restraints can be applied in Sander.
Here's an example of temperature control; note the "&rst iat=0, &end" that ends the section:
Run belly water at 300K to disorder wat216 periodicity then cool
&cntrl irest=0, ntx=1, ibelly=1,
imin=0, nrun=1, nstlim=2000, nsnb=25,
tempi=10.0, temp0=300.0, ntt=1, npscal=1,
ntc=2, ntf=2, cut=8.0, ntb=1,
nmropt=1, iftres=0,
&end
# Warm up fast (actual temp will take a while) then after a while, cool down.
# ATOM numbers need to be set for each system, e.g. 1st ion, last water atom.
&wt type='TEMP0', istep1=1000, istep2=2000,
value1=300.0, value2=10.0, iinc=5, &end
&wt type='END', &end
&rst iat=0, &end
belly - waters, ions
ATOM 531 9030
END
END
How to get cartesian and NMR restraints together?
Put the nmr restraints into a DISANG file; they unfortunately cannot be in the mdin file itself.
Section Four of Sander input in the Amber 7 manual [Distance, angle,
and torsional restraints] describes how to restrain, not constrain,
dihedrals.
There is no way to keep torsion angles absolutely fixed
within AMBER. Incidentally, you can
easily create a
Dave Case:
Yes. The variable IFVARI can be used to control individual restraint
weights. See section 5.9 of the Amber 7 manual. For example, if you wanted to have
a WC constraint on for the first 2500 steps, then ramp to zero during
the next 2500 steps, you might do something like the following:
Refc cannot be used for internal (bond, angle or dihedral) constraints:
it is for Cartesian restraints only. The format is the same as
inpcrd and restrt.
R1, R2, R3, R4 define a flat-welled parabola which becomes linear beyond
a specified distance. I.e.
Answer is in the manual, but somewhat hidden! See the discussion
about the "IPNLTY" variable:
Further discussion appears in section SIX, "Chemical Shift Restraints".
Basically, the program will minimize the sum of the absolute values of
the "errors", where in this case the "error" is the difference between
the calculated and the observed shift. The SHRANG variable allows you
to ignore errors less than some cutoff, and the WT variable allows you
to weight some shifts more heavily than others in the sum.
Positional restraints work well enough to keep a molecule near
its starting conformation, and they can force a molecule from one
conformation to a second SIMILAR conformation. But they don't do
a good job of forcing a molecule through substantial
regions of conformational or distance space.
See src/nmr_aux/prepare_input/makeCHIR_RST.
This script will construct penalty functions to help keep all chiral carbons
in the right places, even under high-T annealling.
Is it possible to operate two independent sets of distance angle
restraints, allowing both to be initially ramped in and then
after 20-25ps the [e.g.] Watson/Crick distance and angle restraints to
be slowly removed leaving the NMR derived restraints in place ??
&rst iat=?,?, r1=???, r2=???, r3=???, r4=???, rk2=???, rk3=???,
nstep1=0, nstep2=2500, &end
&rst iat=?,?, nstep1=2501, nstep2=5000, ifvari=1,
r1a=???, r2a=???, r3a=???, r4a=???, rk2a=0.0, rk3a=0.0, &end
The first &rst line sets up the constraint for the first 2500 steps, and
it is constant (ifvari has the default value of zero.) The second &rst
continues this constraint for another 2500 steps, but ramps the force
constants rk2 and rk3 down to zero; as these get smaller, there essentially
becomes no penalty for violating the constraint. After 5000 steps, neither
constraint is active.
How can we make the file 'refc' for running with internal
constraints?
Please explain distance restraints in sander.
\ /
\ /
\ /
. .
. .
._______.
R1 R2 R3 R4
"\" = lower bound linear response region
"/" = lower bound linear response region
"." = parobola
"_" = flat region
If you have determined lower and upper bounds from an NMR experiment,
those would typically correspond to R2 and R3. Note that the flat well
means that any value R2 <= value <= R3 is equally acceptable. R1 and
R4 define linear response regions. These are sometimes used so that
restraints that severely violate the lower and upper bounds don't
tear the structure up. A typical value of R1 is R2-2.0. And a typical
value of R4 is R3+2.0 (angstroms).
What is the form of the potential used for chemical shift restraints?
IPNLTY
= 1 the program will minimize the sum of the
absolute values of the errors; this is
akin to minimizing the crystallographic R-
factor (default).
= 2 the program will optimize the sum of the
squares of the errors.
= 3 For NOESY intensities, the penalty will be
of the form
awt [Ic^(1/6)-Io^(1/6)]^2.
Chemical shift penalties will be as for
ipnlty=1.
(5.11 page 119 in Amber7 manual)
How about using positional restraints to force conformational changes?
Is there a way Amber/Sander rtMD simulation can
be restrained so that D amino acids are forbidden
even though I have bad NMR restraints?