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
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