Unknown coordinates error during SA

[Aaron Oakley]

>  Anyone has an explanation how this error can occur? 
>  It occurs only after reaching a higher temperature during
>  simulated annealing. Thanks.
> 
>  %ATMCHK-ERR: unknown coordinates for atom "    -1066-MET -H   "
>  %ATMCHK-ERR: unknown coordinates for atom "    -1071-GLN -HE22"
>  %ATMCHK-ERR: unknown coordinates for atom "    -1098-VAL -O   "
>  %ATMCHK-ERR: unknown coordinates for atom "    -1102-ILE -H   "
>  %ATMCHK-ERR: unknown coordinates for atom "    -1124-GLY -H   "
>  %ATMCHK-ERR: unknown coordinates for atom "    -1147-PHE -H   "
>  %ATMCHK-ERR: Unknown coordinates
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>  BOMLEV=    0 reached.  Program execution will be terminated.
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

As I understand it, this error means that your protein has
"exploded", i.e the atoms have "flown off into space".
Try doing a few cycles of 
"repulsion" during your prepstage run. Include the following before the
prepstage minimisation:

{initial minmization has repel nonbonded energy turned on}

 parameter nbonds repel=0.89 rcon=4. end end

 minimize powell
        nstep=40
        drop=40.0
 end

{repel nonbonded eneregy term turned off}

 parameter nbonds repel=0.0 end end

.
.
.
and then the normal minimisation.

Cheers,

Aaron