[gmx-users] help with distance restraints

[Owen, Michael]

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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