[gmx-users] Distance restraints not working

[Justin A. Lemkul]

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

-- 
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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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