RosettaMatch Problem

[Anonymous]

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.

[Author]

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