Hi, all.
I want to refine a PDB file with one zinc ion using 'SetupMetalsMover'.
I have added one zinc ion which is predicted to coordinate with cysteine and histidine.
I noticed there is 'CYZ.params' file and 'residue_types.txt' file ( '/database/chemical/residue_type_sets/fa_standard/residue_types.txt' file ) includes the 'CYZ.params'.
Then, I changed the residue name of cysteine to 'CYZ' (from CYS).
And then, I executed rosettascript to refine my pdb.
But, error has occured and showed as below.
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core.chemical.GlobalResidueTypeSet: (0) {0} Loading (but possibly not actually using) 'CYZ' from the PDB components dictionary for residue type 'pdb_CYZ'
core.io.pose_from_sfr.PoseFromSFRBuilder: (0) {0} Adding undetected upper terminus type to residue 44, 44 A
core.io.pose_from_sfr.PoseFromSFRBuilder: (0) {0} Adding undetected upper terminus type to residue 99, 99 A
core.io.pose_from_sfr.PoseFromSFRBuilder: (0) {0} [ WARNING ] discarding 6 atoms at position 45 in file TaCA_zinc_input.pdb. Best match rsd_type: pdb_CYZ
core.io.pose_from_sfr.PoseFromSFRBuilder: (0) {0} [ WARNING ] discarding 6 atoms at position 100 in file TaCA_zinc_input.pdb. Best match rsd_type: pdb_CYZ
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: OXT on residue THR:CtermProteinFull 44
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C1 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C2 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C3 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C4 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C5 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C6 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C7 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C8 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: N1 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: S1 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C9 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C10 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: N2 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C11 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C12 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C13 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C14 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: CL on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: S2 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: O1 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: O2 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: O3 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: O4 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: N3 on residue pdb_CYZ 45
ERROR: too many tries in fill_missing_atoms!
ERROR:: Exit from: src/core/conformation/Conformation.cc line: 1855
Error: (0) {0} [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'input_0001'
Error: (0) {0} [ ERROR ] Treating failure as bad input; canceling similar jobs
[ ERROR ]: Caught exception:
File: src/core/conformation/Conformation.cc:1855
[ ERROR ] UtilityExitException
ERROR: too many tries in fill_missing_atoms!
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I guess I might have lost something, but I don't know what it is...
I'm using 'Rosetta 2021.38'.
Any suggestion would be greatly appreciated.
Thanks all.