[gmx-users] Distance restraints not working

Thomas Grant tgrant at hwi.buffalo.edu
Tue May 22 21:25:19 CEST 2012

Dear all,

I am attempting to keep a Zn ion in place in a zinc finger motif using
distance restraints to the coordinating cysteine residues.  The zinc is
structural and not catalytic, and it was suggested from this list that
using distance restraints should suffice without the need for

Unfortunately after several tries the distance restraints don't appear to
be applied after 100 ps of isothermal-isochoric equilibration, however it
did seem to work for the minimization step.  My topology file contains the

#ifdef DISRES
[ distance_restraints ]
; ai   aj   type index typeâ low up1 up2 fac
  13082 5576 1    0     1     0.0 0.23 0.3 10000.0
  13082 5604 1    1     1     0.0 0.23 0.3 10000.0
  13082 5959 1    2     1     0.0 0.23 0.3 10000.0
  13082 5993 1    3     1     0.0 0.20 0.3 10000.0

and my .mdp file has the following two lines inserted:

define          = -DDISRES      ; distance restrain the protein
disre           = simple        ; Enable Distance Restraints

I first attempted to use small factors to multiply the restraints, 1, 2,
10, but nothing seemed to be working so I just put an extreme value of
10,000 to ensure the energy contribution from the restraints would dominate
and keep the zinc in place, but that still didn't seem to do the trick
which makes me think that there's some other error I'm missing.  I checked
my .gro file to ensure that the atom indices were correct and they are.  I
also have ensured that the zinc ion and coordinating cysteines are part of
the same chain. The zinc appears to move by about 4 Å to be coordinated by
a nearby glutamate instead.

Any ideas on why the restraints don't seem to be working?


Thomas D. Grant
Graduate Research Assistant
Hauptman-Woodward Medical Research Institute
700 Ellicott St.
Buffalo, NY 14203
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