Hello, I am trying to protonate at ADP molecule with modeller6. THe ADP residue is specified in the library, but I keep getting this error:
gener___479E> Must not use patching residues here. Residue type index, residue type: 33 # recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Here is the script for the protonation: # This will read a specified atom file, generate all hydrogen atoms, # add atomic radii and charges, and write the model to a PDB file in # the GRASP format. This can be used with GRASP to display electrostatic # properties without assigning charges and radii in GRASP. INCLUDE SET TOPLIB = '$(LIB)/TOP.LIB' SET PARLIB = '$(LIB)/PAR.LIB' READ_TOPOLOGY FILE = '$(LIB)/TOP.LIB' READ_PARAMETERS FILE = '$(LIB)/PAR.LIB' SET TOPOLOGY_MODEL = 1, HYDROGEN_IO = on, HETATM_IO = on, WATER_IO = on SET ATOM_FILES_DIRECTORY = './' # directories for input atom files READ_MODEL FILE = 'adp.pdb' RENAME_SEGMENTS SEGMENT_IDS = 'A' SEQUENCE_TO_ALI ATOM_FILES = 'adp', ALIGN_CODES = 'adp' SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES 'adp.pdb', ; ALIGN_CODES = ALIGN_CODES 'adp' GENERATE_TOPOLOGY SEQUENCE = 'adp' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off, BUILD_METHOD = 'INTERNAL_COORDINATES' WRITE_MODEL FILE = 'protoadp.pdb', MODEL_FORMAT = 'GRASP'
And here is the ADP PDB File:
HETATM 569 PB ADP X 68 14.423 48.400 0.539 HETATM 570 O1B ADP X 68 15.523 47.578 -0.057 HETATM 571 O2B ADP X 68 14.303 48.106 2.067 HETATM 572 O3B ADP X 68 14.698 49.918 0.358 HETATM 573 PA ADP X 68 11.796 47.376 0.153 HETATM 574 O1A ADP X 68 12.031 45.921 0.312 HETATM 575 O2A ADP X 68 11.228 48.083 1.373 HETATM 576 O3A ADP X 68 13.146 48.057 -0.376 HETATM 577 O5' ADP X 68 10.874 47.635 -1.110 HETATM 578 C5' ADP X 68 11.196 47.105 -2.379 HETATM 579 C4' ADP X 68 10.286 47.636 -3.486 HETATM 580 O4' ADP X 68 9.080 46.895 -3.526 HETATM 581 C3' ADP X 68 9.861 49.060 -3.289 HETATM 582 O3' ADP X 68 9.602 49.725 -4.510 HETATM 583 C2' ADP X 68 8.559 48.875 -2.526 HETATM 584 O2' ADP X 68 7.781 49.993 -2.657 HETATM 585 C1' ADP X 68 7.956 47.654 -3.193 HETATM 586 N9 ADP X 68 7.087 46.896 -2.257 HETATM 587 C8 ADP X 68 7.503 45.956 -1.333 HETATM 588 N7 ADP X 68 6.392 45.519 -0.679 HETATM 589 C5 ADP X 68 5.314 46.174 -1.216 HETATM 590 C6 ADP X 68 3.977 46.114 -0.937 HETATM 591 N6 ADP X 68 3.529 45.338 0.072 HETATM 592 N1 ADP X 68 3.138 46.928 -1.662 HETATM 593 C2 ADP X 68 3.573 47.780 -2.658 HETATM 594 N3 ADP X 68 4.896 47.853 -2.965 HETATM 595 C4 ADP X 68 5.741 47.039 -2.222
Any ideas why this won't work?
Thanks kindly,
Karl Schweighofer karl@mail.arc.nasa.gov