On 5/22/12 9:25 PM, Thomas Grant wrote:
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 reparameterization.
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 following:
#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
#endif
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?
There are a few possibilities.
1. Numbering in [distance_restraints] is not based on .gro numbering. The atom
numbers supplied are only relevant within the [moleculetype] to which they
belong, much like [position_restraints]. Also make sure that the
[distance_restraints] block is in the correct location in the topology.
2. You've omitted the dihre_fc keyword, though it is set to 1000 by default.
Check the mdout.mdp file or your .tpr file to ensure that you have a sensible
value here. Setting values of fac that high are unnecessary.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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