Hi all,
Sorry for sparing your time. I am a rookie trying to use the RosettaMatch to design some zinc binding position inside a helical structure. Once I typed in the following command, there is always something wrong while I cannot figure out why.
Once I typed:
dawei@dawei-T5610:~/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin$ ./match.static.linuxgccrelease -s czy.pdb -match::lig_name ZNX -match::grid_boundary czy.gridlig -match::scaffold_active_site_residues czy.pos -match::geometric_constraint_file ZNX.cst -match::output_matchres_only -extra_res_fa ZNX.params -output_matches_per_group 10 -ex1 -ex2 -euclid_bin_size 1.0 -euler_bin_size 10.0 -bump_tolerance 0.5 -match:output_format PDB -match:consolidate_matches -match:output_matchres_only
It always shows:
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534
core.init: command: ./match.static.linuxgccrelease -s czy.pdb -match::lig_name ZNX -match::grid_boundary czy.gridlig -match::scaffold_active_site_residues czy.pos -match::geometric_constraint_file ZNX.cst -match::output_matchres_only -extra_res_fa ZNX.params -output_matches_per_group 10 -ex1 -ex2 -euclid_bin_size 1.0 -euler_bin_size 10.0 -bump_tolerance 0.5 -match:output_format PDB -match:consolidate_matches -match:output_matchres_only
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1694670699 seed_offset=0 real_seed=-1694670699
core.init.random: RandomGenerator:init: Normal mode, seed=-1694670699 RG_type=mt19937
core.init: Resolved executable path: /home/dawei/rosetta_bin_linux_2018.33.60351_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/static/match.static.linuxgccrelease
core.init: Looking for database based on location of executable: /home/dawei/rosetta_bin_linux_2018.33.60351_bundle/main/database/
core.chemical: [ WARNING ] Ignoring line starting with ' NAME' when parsing topology file.
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 618 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.87 seconds.
core.import_pose.import_pose: File 'czy.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 120
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 240
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 360
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 480
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 600
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 720
ERROR: The residue ZNX could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)
ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 123
BACKTRACE:
[0x5cdddd8]
[0x577d0d2]
[0x623d80]
[0x4113af]
[0x61d5a24]
[0x62396d]
caught exception
File: src/core/chemical/ResidueTypeSet.cc:123
[ ERROR ] UtilityExitException
ERROR: The residue ZNX could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)
The ZNX.cst and ZNX.params files were directly obtained from a JACS paper: Der, Bryan S., et al. "Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer." Journal of the American Chemical Society 134.1 (2011): 375-385.
ZNX.cst file:
#block 1 of 2
VARIABLE_CST::BEGIN
#Block 1 His, trying to make it work for both NE2 and ND1 at the same time
(torsion_AB = 0 +/- 180)
CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_name: ZN V1 V2
TEMPLATE:: ATOM_MAP: 1 residue3: ZN
TEMPLATE:: ATOM_MAP: 2 atom_type: Nhis
TEMPLATE:: ATOM_MAP: 2 residue3: HIS
CONSTRAINT:: distanceAB: 2.05 0.15 40.0 0
CONSTRAINT:: angle_A: 109.5 15.0 40.0 360.
CONSTRAINT:: angle_B: 125.0 15.0 40.0 360.
CONSTRAINT:: torsion_A: 0.0 15.0 40.0 10.0
CONSTRAINT:: torsion_AB: 60.0 15.0 40.0 120.
CONSTRAINT:: torsion_B: 0.0 15.0 40.0 180.
CST::END
#Block 1 Cys
CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_name: ZN V1 V2
TEMPLATE:: ATOM_MAP: 1 residue3: ZN
TEMPLATE:: ATOM_MAP: 2 atom_type: S
TEMPLATE:: ATOM_MAP: 2 residue1: C
CONSTRAINT:: distanceAB: 2.33 0.15 40.0 0
CONSTRAINT:: angle_A: 109.5 15.0 40.0 360.
CONSTRAINT:: angle_B: 109.5 15.0 40.0 360.
CONSTRAINT:: torsion_A: 0.0 15.0 40.0 10.0
CONSTRAINT:: torsion_AB: 60.0 15.0 40.0 120.
CONSTRAINT:: torsion_B: 0.0 15.0 40.0 10.0
CST::END
VARIABLE_CST::END
ZNX.params file:
NAME ZNX
IO_STRING ZNX Z
TYPE LIGAND
AA UNK
ATOM ZN Zn2p X 2.0
ATOM V1 VIRT X 0.0
ATOM V2 VIRT X 0.0
ATOM V3 VIRT X 0.0
ATOM V4 VIRT X 0.0
BOND ZN V1
BOND ZN V2
BOND ZN V3
BOND ZN V4
NBR_ATOM ZN
NBR_RADIUS 0.0
ICOOR_INTERNAL V1 0.000000 0.000000 0.000000 V1 ZN V2
ICOOR_INTERNAL ZN 0.000000 0.000000 1.000000 V1 ZN V2
ICOOR_INTERNAL V2 0.000000 70.500000 1.000000 ZN V1 V2
ICOOR_INTERNAL V3 -120.000000 70.500000 1.000000 ZN V1 V2
ICOOR_INTERNAL V4 120.000000 70.500000 1.000000 ZN V1 V2
I am wodering if someone can help me out here. Many thanks to you.