[gmx-users] help with distance restraints

[Arthur Roberts]

Hi, Michael,

1) add Cu2+ the [atoms], [bonds], etc sections in the
.top file.
2) you need to change all the entries in the residue
column of the [atoms] section to the same name (e.g.
MOL) in both the top file and the gro file, including
all the residues of the protein.  Gromacs needs to
think that it is one big molecule.

Then the distance restraints will work fine.  I made a
script file in python to change all the entries to the
same name.

Change the [ molecules ] section to reflect that the
protein and the Cu2+ is treated as one molecule.

e.g.

[ molecules ]
; Compound        #mols
Protein             1          
SOL             88367
Cu2+                1

to 

[ molecules ]
; Compound        #mols
MOL                 1
SOL             88367

Good Luck,
Art


--- "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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