explicit solvent?

[ever4cyth]

Tried 1be9.pdb as in the tutorial, amber with implicit solvent runs ok, but looks like there is problem whenever explicit solvent is used.

min.grompp.log
Program grompp, VERSION 4.6.3

Fatal error:
[ file min_posre.itp, line 710 ]:
Atom index (1796) in position_restraints out of bounds (1-1795).
This probably means that you have inserted topology section "position_restraints"
in a part belonging to a different molecule than you intended to.

min.namd2.log
FATAL ERROR: Number of atoms in constraint reference PDB doesn't match coordinate PDB
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Number of atoms in constraint reference PDB doesn't match coordinate PDB

Charm++ fatal error:
FATAL ERROR: Number of atoms in constraint reference PDB doesn't match coordinate PDB

[boscoh]

Can you tell me the commands you used?