fgrunewald
commented
1 year ago @bwbai please note that the beta martini3 version is not correctly handling parameters for protonated AAs and/or HIS tautomers. If you use the final version (i.e. martini3001) instead you will get the correct parameters. Should you want to run with the beta version the best fix is to install the previous version from pypi for example.
hey everyone, Please suggest some alternative solutions that could fix this issue. Thanks a lot.
martinize2 -f /mnt/d/desktop/drot1/drot1.pdb -dssp dssp -scfix -o topol.top -x drot1_CG.pdb -ff martini30b32 -nt -maxwarn 9ERROR - general - Modification HSP in force field None is not a single connected component INFO - general - Read 1 molecules from PDB file /mnt/d/desktop/drot1/drot1.pdb INFO - step - Guessing the bonds. INFO - general - 1 molecules after guessing bonds INFO - step - Repairing the graph. INFO - general - Applying modification NH2-ter to residue A-MET1 INFO - general - Applying modification COOH-ter to residue A-ALA425 INFO - step - Dealing with modifications. INFO - general - Identified the modifications ['NH2-ter'] on residues ['MET1', 'MET1', 'MET1', 'MET1'] INFO - general - Identified the modifications ['COOH-ter'] on residues ['ALA425', 'ALA425', 'ALA425'] INFO - step - Read input. INFO - step - Creating the graph at the target resolution. WARNING - unmapped-atom - Can't find modification mappings for the modifications ['NH2-ter']. The following modification mappings are known: {('C-ter',): <vermouth.map_parser.Mapping object at 0x7f7c7e27e400>, ('N-ter',): <vermouth.map_parser.Mapping object at 0x7f7c7e22f8e0>} WARNING - unmapped-atom - Can't find modification mappings for the modifications ['COOH-ter']. The following modification mappings are known: {('C-ter',): <vermouth.map_parser.Mapping object at 0x7f7c7e27e400>, ('N-ter',): <vermouth.map_parser.Mapping object at 0x7f7c7e22f8e0>} WARNING - unmapped-atom - These atoms are not covered by a mapping. Either your mappings don't describe all atoms (bad idea), or, there's no mapping available for all residues. ['3294A-ALA425:OXT'] INFO - step - Averaging the coordinates. INFO - step - Applying the links. INFO - step - Placing the charge dummies. INFO - step - Writing output. INFO - general - Please cite: Souza, P C T; Marrink, S J; 2020 ERROR - general - 1 warnings were encountered after accounting for the -maxwarn flag. No output files will be written. Consider fixing the warnings, or if you are sure they are harmless, use the -maxwarn flag.