[gmx-users] Distance restraints

[David Mobley]

If I remember correctly, distance restraints (for some reason) only
work between multiple atoms of the same "molecule". By molecule, I
don't mean that they have to be joined by bonds; rather, both need to
appear in the same [ moleculetype ] section of the topology, which
means that GROMACS considers them a "molecule".

The other way of thinking of this is that distance restraints use the
atom numbers from the [ atoms ] section that they follow. If you're
trying to use the atom numbers from your gro file, it won't work;
GROMACS won't understand them. So in your case, it means you need to
get the parameters for your ions out of your ions.itp file and insert
explicit ions with atom numbers into the appropriate sections of your
topology, following the peptide atoms, probably.

I hope that makes sense. Search the mailing list on distance
restraints if you need more; this has been discussed on thel ist
before.

David

On 8/3/06, Owen, Michael <MichaelOwen at creighton.edu> wrote:
>
>
>
>
> Hello,
>
>  I am trying to use NMR restraints to position a Cu2+ ion around specific
> residues of a peptide.  I added Cu2+ using "genion" and then initiated
> "grompp" before an energy minim minimization.  I received the following
> error message while executing "grompp":
>
>
>  -------------------------------------------------------
>  Program grompp, VERSION 3.3.1
>  Source code file: toppush.c, line: 1108
>
>  Fatal error:
>  [ file "Ab_Cu.top", line 5864 ]:
>               Atom index (67248) in distance_restraints out of bounds (1-1)
>  -------------------------------------------------------
>
>
>  Below is the entry in the topology file.  Line 5864 contains the value 97
> and the value 67248 refers is the atom number of the Cu2+ ion.
>
>
>  [ distance_restraints ]
>
>  ;ai     aj      type    index   type'   low     up1     up2     fac
>  67248   97      1       1       1       0.185   0.195   0.2     1.0
>  67248   196     1       1       1       0.185   0.195   0.2     1.0
>  67248   213     1       1       1       0.185   0.195   0.2     1.0
>  67248   148     1       1       1       0.195   0.205   0.21    1.0
>
>  Could you suggest any changes that would eliminate my error?
>
>  Thanks in advance,
>
>  Michael Owen
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