I am trying to run enzyme design on one of the models that I got from a matcher run, but it fails with the following:
protocols.toolbox.match_enzdes_util.EnzConstraintParameters: for block 1, 1 newly generated constraints were added
protocols.toolbox.match_enzdes_util.EnzConstraintIO: checking cst data consistency for block 1... done
protocols.toolbox.match_enzdes_util.EnzConstraintIO: Cst Block 1done...
protocols.toolbox.match_enzdes_util.EnzConstraintParameters: for block 2, 1 newly generated constraints were added
protocols.toolbox.match_enzdes_util.EnzConstraintIO: checking cst data consistency for block 2... done
protocols.toolbox.match_enzdes_util.EnzConstraintIO: Cst Block 2done...
protocols.toolbox.match_enzdes_util.EnzConstraintParameters: for block 3, 1 newly generated constraints were added
protocols.toolbox.match_enzdes_util.EnzConstraintIO: checking cst data consistency for block 3... done
protocols.toolbox.match_enzdes_util.EnzConstraintIO: Cst Block 3done...
ERROR: unknown atom_name: LYS 1HZ
ERROR:: Exit from: src/core/chemical/ResidueType.cc line: 1645
protocols.toolbox.match_enzdes_util.EnzConstraintIO: checking cst data consistency for block 4...
Here is the cst block; it worked for matcher, without issue:
CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_name: N2 FE1 S2
TEMPLATE:: ATOM_MAP: 1 residue3: HAS
TEMPLATE:: ATOM_MAP: 2 atom_name: NZ CE 1HZ
TEMPLATE:: ATOM_MAP: 2 residue1: K
CONSTRAINT:: distanceAB: 2.85 0.10 0.00 1 1
CONSTRAINT:: angle_A: 110.00 7.00 0.00 360.00 2
CONSTRAINT:: angle_B: 109.50 15.00 0.00 360.00 2
CONSTRAINT:: torsion_B: 0.00 5.00 0.00 360.00 1
ALGORITHM_INFO:: match
SECONDARY_MATCH: DOWNSTREAM
CHI_STRATEGY:: CHI 1 EX_TWO_HALF_STEP_STDDEVS
CHI_STRATEGY:: CHI 2 EX_ONE_STDDEV
ALGORITHM_INFO::END
CST::END
Why doesn't enzyme design recognize an atom name for a standard amino acid? Here is the beginning of the parameter file (rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/LYS.params):
#rosetta residue topology file
#version 0.1
NAME LYS
IO_STRING LYS K
TYPE POLYMER #residue type
AA LYS
ATOM N Nbb NH1 -0.47
ATOM CA CAbb CT1 0.07
ATOM C CObb C 0.51
ATOM O OCbb O -0.51
ATOM CB CH2 CT2 -0.18
ATOM CG CH2 CT2 -0.18
ATOM CD CH2 CT2 -0.18
ATOM CE CH2 CT2 0.21
ATOM NZ Nlys NH3 -0.3
ATOM H HNbb H 0.31
ATOM 1HZ Hpol HC 0.33
ATOM 2HZ Hpol HC 0.33
ATOM 3HZ Hpol HC 0.33
ATOM HA Hapo HB 0.09
ATOM 1HB Hapo HA 0.09
ATOM 2HB Hapo HA 0.09
ATOM 1HG Hapo HA 0.09
ATOM 2HG Hapo HA 0.09
ATOM 1HD Hapo HA 0.09
ATOM 2HD Hapo HA 0.09
ATOM 1HE Hapo HA 0.05
ATOM 2HE Hapo HA 0.05
Thanks for your help.
We typically don't match or constrain on hydrogen atoms. (There's some complications due to the fact that there's three hydrogen atoms on that nitrogen, and we don't really sample them as distinct entities - so you might miss out on rotamers where it's 2NZ that's in the correct orientation.) That said, it shouldn't result in an error message.
One possibility is that there's some non-printing character that's coming before/after the 1HZ in the constraints file that's causing issues looking up the atom name. Try deleteing that line and retyping it from scratch (no copy-paste, as you may inadvertently copy the non-printing character), being sure to add several spaces after the 1HZ (to separate it from potential line-ending noise).