Difficulty to martinize #612

amiel-ab · 2024-09-12T11:01:27Z

amiel-ab
Sep 12, 2024

Dear developers,

I am trying to martinize this complex and I am not sure as to why it seems struggling to do so;. The log seems to point out inconsistency of data and I think it is might due to wrong formatting but I don't know exactly where ?
Do you have any ideas ?

Thanks

tn_prot_only.zip

Answered by amiel-ab

Sep 25, 2024

It is solved, the problem is that martinize get confused because this is a big system there are many chains (that is why clicking on one residue in Pymol will select multiple residues), so the way to do it is (by scripting) separate the PDB with different chains ans subchains so that we can martinize it separately ; and after we can combine the topologies.
Thank you for the help.

View full answer

pckroon · 2024-09-12T14:51:10Z

pckroon
Sep 12, 2024
Maintainer

Hello hello!
Do you have the command line invocation you use and the corresponding screen output for me?

6 replies

pckroon Sep 13, 2024
Maintainer

Could you copy/paste (rather than screenshot) the complete screen output? Also, this output cannot be generated with this command line: level 5 log messages don't get printed by default.

amiel-ab Sep 13, 2024
Author

Indeed, my bad I also used the -vv flag.

It freezes at this point : DEBUG - step - vermouth.processors.repair_graph - Matching residue A-MET1 to its reference

Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF slipids
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF slipids
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF slipids
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPC for FF amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block DMPC for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block DMPC for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block DMPC for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block DMPC for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block DMPC for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block DMPC for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block DMPC for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block DMPC for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block DMPC for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block DMPC for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block DMPC for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block DMPC for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPG for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPG for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPG for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPG for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPG for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPG for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPG for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPG for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPG for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HD1 in block HIS in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HD1 in block HIS in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HD1 in block HIS in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPE for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPE for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPE for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPE for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPE for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPE for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPE for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPE for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPE for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPS for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPS for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPS for FF charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block POPS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF universal
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HZ1 in block LYS in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HZ2 in block LYS in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HZ3 in block LYS in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HE11 in block GLN in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HE12 in block GLN in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HE2 in block HSD in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HSD for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HSD for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HE2 in block GLU in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HD1 in block HIS in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HD2 in block ASP in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block LYN in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HZ3 in block LYN in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block LYN in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HZ3 in block LYN in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block VAL in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block MET in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block HIP in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIP for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIP for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block TRP in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block ILE in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HE11 in block GLN in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HE12 in block GLN in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block PHE in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PHE for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block MET for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block SER in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HG1 in block SER in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HSP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HSP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASPP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASPP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block CYS in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HG1 in block CYS in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block CYS for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block ASP in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HD2 in block ASP in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HE2 in block HSD in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HSD for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HSD for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block ASH in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block ASH in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block GLU in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HE2 in block GLU in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block TYR in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TYR for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block THR in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ILE for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block HIS in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HE2 in block HIS in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block LYS in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block LEU in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block HIE in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HD1 in block HIE in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIE for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIE for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block GLN in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HE11 in block GLN in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HE12 in block GLN in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block GLH in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block GLH in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HD1 in block HSE in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HSE for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HSE for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block ARG in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LEU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block PRO for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block GLY in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLY for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HE2 in block GLU in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block ALA in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ALA for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HD1 in block HIS in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block HIS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block TRP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HZ3 in block LSN in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LSN for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LSN for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLUP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLUP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HN in block ASN in force field amber
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF amber27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF amber36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HD2 in block ASP in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HZ1 in block LYS in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HZ2 in block LYS in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HZ3 in block LYS in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block LYS for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HE11 in block GLN in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find atom HE12 in block GLN in force field charmm
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLN for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block THR for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ARG for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block GLU for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASN for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block SER for FF charmm36
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm27
 Level 5 - inconsistent-data - vermouth.map_input - Can't find block ASP for FF charmm36
DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95946D-PRO8:CD and 95947D-PRO8:HD1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95946D-PRO8:CD and 95948D-PRO8:HD2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95946D-PRO8:CD and 95954D-PRO8:CG based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95949D-PRO8:CA and 95950D-PRO8:HA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95949D-PRO8:CA and 95951D-PRO8:CB based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95949D-PRO8:CA and 95957D-PRO8:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95951D-PRO8:CB and 95952D-PRO8:HB1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95951D-PRO8:CB and 95953D-PRO8:HB2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95951D-PRO8:CB and 95954D-PRO8:CG based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95957D-PRO8:C and 95959D-ARG9:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95959D-ARG9:N and 95960D-ARG9:HN based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95959D-ARG9:N and 95961D-ARG9:CA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95961D-ARG9:CA and 95981D-ARG9:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95963D-ARG9:CB and 95966D-ARG9:CG based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95966D-ARG9:CG and 95969D-ARG9:CD based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95969D-ARG9:CD and 95970D-ARG9:HD1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95969D-ARG9:CD and 95971D-ARG9:HD2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95969D-ARG9:CD and 95972D-ARG9:NE based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95974D-ARG9:CZ and 95975D-ARG9:NH1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95974D-ARG9:CZ and 95978D-ARG9:NH2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95978D-ARG9:NH2 and 95979D-ARG9:HH21 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95978D-ARG9:NH2 and 95980D-ARG9:HH22 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95981D-ARG9:C and 95983D-TYR10:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96002D-TYR10:C and 96004D-ARG11:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96026D-ARG11:C and 96028D-GLU12:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96041D-GLU12:C and 96043D-LEU13:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96045D-LEU13:CA and 96060D-LEU13:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96050D-LEU13:CG and 96056D-LEU13:CD2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96052D-LEU13:CD1 and 96055D-LEU13:HD13 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96056D-LEU13:CD2 and 96057D-LEU13:HD21 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96056D-LEU13:CD2 and 96058D-LEU13:HD22 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96056D-LEU13:CD2 and 96059D-LEU13:HD23 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96060D-LEU13:C and 96061D-LEU13:O based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96060D-LEU13:C and 96062D-ALA14:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96070D-ALA14:C and 96072D-ARG15:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96072D-ARG15:N and 96073D-ARG15:HN based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96072D-ARG15:N and 96074D-ARG15:CA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96074D-ARG15:CA and 96094D-ARG15:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96079D-ARG15:CG and 96080D-ARG15:HG1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96079D-ARG15:CG and 96081D-ARG15:HG2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96079D-ARG15:CG and 96082D-ARG15:CD based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96082D-ARG15:CD and 96083D-ARG15:HD1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96082D-ARG15:CD and 96084D-ARG15:HD2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96082D-ARG15:CD and 96085D-ARG15:NE based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96085D-ARG15:NE and 96086D-ARG15:HE based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96085D-ARG15:NE and 96087D-ARG15:CZ based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96087D-ARG15:CZ and 96088D-ARG15:NH1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96087D-ARG15:CZ and 96091D-ARG15:NH2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96088D-ARG15:NH1 and 96090D-ARG15:HH12 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96094D-ARG15:C and 96095D-ARG15:O based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96094D-ARG15:C and 96096D-ASN16:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96108D-ASN16:C and 96110D-TRP17:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96132D-TRP17:C and 96134D-ILE18:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96151D-ILE18:C and 96153D-PRO19:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96165D-PRO19:C and 96167D-THR20:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96167D-THR20:N and 96168D-THR20:HN based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96169D-THR20:CA and 96170D-THR20:HA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96169D-THR20:CA and 96171D-THR20:CB based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96169D-THR20:CA and 96179D-THR20:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96171D-THR20:CB and 96172D-THR20:HB based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96171D-THR20:CB and 96173D-THR20:OG1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96171D-THR20:CB and 96175D-THR20:CG2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96173D-THR20:OG1 and 96174D-THR20:HG1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96175D-THR20:CG2 and 96176D-THR20:HG21 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96175D-THR20:CG2 and 96177D-THR20:HG22 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96175D-THR20:CG2 and 96178D-THR20:HG23 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96179D-THR20:C and 96181D-ALA21:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96181D-ALA21:N and 96182D-ALA21:HN based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96181D-ALA21:N and 96183D-ALA21:CA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96183D-ALA21:CA and 96184D-ALA21:HA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96183D-ALA21:CA and 96185D-ALA21:CB based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96183D-ALA21:CA and 96189D-ALA21:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96185D-ALA21:CB and 96186D-ALA21:HB1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96185D-ALA21:CB and 96187D-ALA21:HB2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96185D-ALA21:CB and 96188D-ALA21:HB3 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96189D-ALA21:C and 96190D-ALA21:O based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96189D-ALA21:C and 96191D-GLY22:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96196D-GLY22:C and 96198D-MET23:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96213D-MET23:C and 96215D-TRP24:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96237D-TRP24:C and 96239D-GLY25:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96244D-GLY25:C and 96246D-THR26:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96258D-THR26:C and 96260D-VAL27:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96260D-VAL27:N and 96261D-VAL27:HN based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96260D-VAL27:N and 96262D-VAL27:CA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96262D-VAL27:CA and 96263D-VAL27:HA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96262D-VAL27:CA and 96264D-VAL27:CB based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96262D-VAL27:CA and 96274D-VAL27:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96264D-VAL27:CB and 96265D-VAL27:HB based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96264D-VAL27:CB and 96266D-VAL27:CG1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96264D-VAL27:CB and 96270D-VAL27:CG2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96266D-VAL27:CG1 and 96267D-VAL27:HG11 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96266D-VAL27:CG1 and 96268D-VAL27:HG12 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96266D-VAL27:CG1 and 96269D-VAL27:HG13 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96270D-VAL27:CG2 and 96273D-VAL27:HG23 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96274D-VAL27:C and 96275D-VAL27:O based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96274D-VAL27:C and 96276D-GLY28:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96276D-GLY28:N and 96277D-GLY28:HN based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96276D-GLY28:N and 96278D-GLY28:CA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96281D-GLY28:C and 96283D-ALA29:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96283D-ALA29:N and 96284D-ALA29:HN based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96283D-ALA29:N and 96285D-ALA29:CA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96285D-ALA29:CA and 96286D-ALA29:HA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96285D-ALA29:CA and 96287D-ALA29:CB based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96285D-ALA29:CA and 96291D-ALA29:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96287D-ALA29:CB and 96288D-ALA29:HB1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96287D-ALA29:CB and 96289D-ALA29:HB2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96287D-ALA29:CB and 96290D-ALA29:HB3 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96291D-ALA29:C and 96292D-ALA29:O based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96291D-ALA29:C and 96293D-VAL30:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96293D-VAL30:N and 96294D-VAL30:HN based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96293D-VAL30:N and 96295D-VAL30:CA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96295D-VAL30:CA and 96296D-VAL30:HA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96295D-VAL30:CA and 96297D-VAL30:CB based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96295D-VAL30:CA and 96307D-VAL30:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96297D-VAL30:CB and 96298D-VAL30:HB based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96297D-VAL30:CB and 96299D-VAL30:CG1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96297D-VAL30:CB and 96303D-VAL30:CG2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96299D-VAL30:CG1 and 96300D-VAL30:HG11 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96299D-VAL30:CG1 and 96301D-VAL30:HG12 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96299D-VAL30:CG1 and 96302D-VAL30:HG13 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96303D-VAL30:CG2 and 96306D-VAL30:HG23 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96307D-VAL30:C and 96308D-VAL30:O based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96307D-VAL30:C and 96309D-GLY31:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96309D-GLY31:N and 96310D-GLY31:HN based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96309D-GLY31:N and 96311D-GLY31:CA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96314D-GLY31:C and 96316D-LEU32:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96318D-LEU32:CA and 96333D-LEU32:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96323D-LEU32:CG and 96329D-LEU32:CD2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96325D-LEU32:CD1 and 96328D-LEU32:HD13 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96329D-LEU32:CD2 and 96330D-LEU32:HD21 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96329D-LEU32:CD2 and 96331D-LEU32:HD22 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96329D-LEU32:CD2 and 96332D-LEU32:HD23 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96333D-LEU32:C and 96334D-LEU32:O based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96333D-LEU32:C and 96335D-VAL33:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96349D-VAL33:C and 96351D-TRP34:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96373D-TRP34:C and 96375D-ALA35:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96375D-ALA35:N and 96376D-ALA35:HN based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96375D-ALA35:N and 96377D-ALA35:CA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96377D-ALA35:CA and 96378D-ALA35:HA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96377D-ALA35:CA and 96379D-ALA35:CB based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96377D-ALA35:CA and 96383D-ALA35:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96379D-ALA35:CB and 96380D-ALA35:HB1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96379D-ALA35:CB and 96381D-ALA35:HB2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96379D-ALA35:CB and 96382D-ALA35:HB3 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96383D-ALA35:C and 96384D-ALA35:O based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96383D-ALA35:C and 96385D-THR36:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96397D-THR36:C and 96399D-ASP37:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96399D-ASP37:N and 96400D-ASP37:HN based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96399D-ASP37:N and 96401D-ASP37:CA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96401D-ASP37:CA and 96409D-ASP37:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96403D-ASP37:CB and 96406D-ASP37:CG based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96409D-ASP37:C and 96410D-ASP37:O based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96409D-ASP37:C and 96411D-TRP38:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96433D-TRP38:C and 96435D-ARG39:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96457D-ARG39:C and 96459D-LEU40:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96476D-LEU40:C and 96478D-ILE41:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96495D-ILE41:C and 96497D-LEU42:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96514D-LEU42:C and 96516D-ASP43:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96516D-ASP43:N and 96517D-ASP43:HN based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96516D-ASP43:N and 96518D-ASP43:CA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96518D-ASP43:CA and 96519D-ASP43:HA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96518D-ASP43:CA and 96526D-ASP43:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96520D-ASP43:CB and 96521D-ASP43:HB1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96520D-ASP43:CB and 96522D-ASP43:HB2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96520D-ASP43:CB and 96523D-ASP43:CG based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96526D-ASP43:C and 96527D-ASP43:O based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96526D-ASP43:C and 96528D-TRP44:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96550D-TRP44:C and 96552D-VAL45:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96552D-VAL45:N and 96553D-VAL45:HN based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96552D-VAL45:N and 96554D-VAL45:CA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96554D-VAL45:CA and 96555D-VAL45:HA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96554D-VAL45:CA and 96556D-VAL45:CB based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96554D-VAL45:CA and 96566D-VAL45:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96556D-VAL45:CB and 96557D-VAL45:HB based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96556D-VAL45:CB and 96558D-VAL45:CG1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96556D-VAL45:CB and 96562D-VAL45:CG2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96558D-VAL45:CG1 and 96559D-VAL45:HG11 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96558D-VAL45:CG1 and 96560D-VAL45:HG12 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96558D-VAL45:CG1 and 96561D-VAL45:HG13 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96562D-VAL45:CG2 and 96565D-VAL45:HG23 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96566D-VAL45:C and 96567D-VAL45:O based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96566D-VAL45:C and 96568D-PRO46:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96580D-PRO46:C and 96582D-TYR47:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96601D-TYR47:C and 96603D-ILE48:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96605D-ILE48:CA and 96620D-ILE48:C based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96607D-ILE48:CB and 96613D-ILE48:CG1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96609D-ILE48:CG2 and 96610D-ILE48:HG21 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96609D-ILE48:CG2 and 96611D-ILE48:HG22 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96609D-ILE48:CG2 and 96612D-ILE48:HG23 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96613D-ILE48:CG1 and 96614D-ILE48:HG11 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96613D-ILE48:CG1 and 96615D-ILE48:HG12 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96613D-ILE48:CG1 and 96616D-ILE48:CD based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96616D-ILE48:CD and 96617D-ILE48:HD1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96616D-ILE48:CD and 96618D-ILE48:HD2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96616D-ILE48:CD and 96619D-ILE48:HD3 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96620D-ILE48:C and 96621D-ILE48:O based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96620D-ILE48:C and 96622D-ASN49:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96634D-ASN49:C and 96636D-GLY50:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96636D-GLY50:N and 96637D-GLY50:HN based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96636D-GLY50:N and 96638D-GLY50:CA based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 96641D-GLY50:C and 96643D-GLY50:OT2 based on distance.
    INFO - general - vermouth.processors.make_bonds - 7 molecules after guessing bonds
   DEBUG - step - vermouth - Annotating required mutations and modifications.
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-TRP113 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-ARG430 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-GLY247 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-HIS457 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-THR715 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-ASP172 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-GLN97 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-LEU606 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-MET459 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-ILE344 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-LYS168 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-GLN113 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-SER96 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-GLU156 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-VAL172 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-VAL143 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-ALA1 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-THR35 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-ARG37 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-ILE31 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-ASP70 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-LEU5 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating A-VAL4 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-LEU84 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-ARG120 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-ASP150 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-ASN189 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-HIS128 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-ASP103 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-LEU94 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-ILE186 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-TYR129 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-THR179 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-ALA123 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-ALA174 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-TYR144 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-PRO60 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-SER6 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-PRO2 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-LYS19 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-HIS31 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-LYS5 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-ASP3 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-GLU2 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating B-ASP39 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-PHE437 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-LEU453 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-MET82 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-PHE181 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-TYR380 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-VAL120 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-LYS325 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-TYR157 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-GLY196 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-LYS111 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-GLU79 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-LYS89 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-PHE38 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-ASN48 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-GLY50 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-GLN36 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-HIS8 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-ALA84 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-PHE183 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-ASP86 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-SER126 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-THR140 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-PRO159 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-HIS164 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-GLU22 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-PRO1 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-LEU2 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-SER123 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating C-SER122 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-PHE437 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-LEU453 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-MET82 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-PHE181 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-TYR380 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-VAL120 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-LYS325 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-TYR157 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-GLY196 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-LYS111 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-GLU79 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-LYS89 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-PHE38 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-TRP53 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-GLN36 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-HIS8 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-ALA84 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-PHE183 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-ASP86 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-SER126 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-THR140 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-HIS164 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-GLU22 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-PRO1 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-ILE6 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-LEU2 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-SER123 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-SER122 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-CYS160 with modification C-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating D-PRO159 with modification N-ter
    INFO - step - vermouth - Repairing the graph.
   DEBUG - step - vermouth.processors.repair_graph - Making reference graph
   DEBUG - step - vermouth.processors.repair_graph - Matching residue A-MET1 to its reference

pckroon Sep 13, 2024
Maintainer

I have the feeling the screen output is still incomplete. I expect more references to A-MET1. The second v from -vv doesn't add too much in this case I think, could you try with -v instead?
Also, could you try the -write-graph flag, and inspect the bonds around the afflicted residue with (for example) pymol?

My guess is that your coordinates are too unreasonable.

amiel-ab Sep 25, 2024
Author

It is solved, the problem is that martinize get confused because this is a big system there are many chains (that is why clicking on one residue in Pymol will select multiple residues), so the way to do it is (by scripting) separate the PDB with different chains ans subchains so that we can martinize it separately ; and after we can combine the topologies.
Thank you for the help.

Answer selected by pckroon

pckroon Sep 25, 2024
Maintainer

Thanks for getting back with the result.
For posterity, you could probably also solve this by inserting TER records between the separate proteins/molecules.

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Difficulty to martinize #612

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Difficulty to martinize #612

amiel-ab Sep 12, 2024

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