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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