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boscoh / pdbremix

analyse PDB files, run molecular-dynamics & analyse trajectories
MIT License
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explicit solvent? #2

Open ever4cyth opened 10 years ago

ever4cyth commented 10 years ago

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 commented 10 years ago

Can you tell me the commands you used?