diff --git a/bin/martinize2 b/bin/martinize2 index 38612bb50..59109787f 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -539,6 +539,13 @@ def entry(): "format: :, :..." ), ) + rb_group.add_argument( + "-ew", + dest="rb_write", + default=False, + action="store_true", + help="Write the elastic network to an external .itp file", + ) go_group = parser.add_argument_group("Virtual site based GoMartini") go_group.add_argument( "-go", @@ -1059,6 +1066,7 @@ def entry(): selector=selector, domain_criterion=domain_criterion, res_min_dist=args.res_min_dist, + write_out=args.rb_write, ) rubber_band_processor.run_system(system) diff --git a/vermouth/gmx/itp.py b/vermouth/gmx/itp.py index 821232c31..3cdce91c3 100644 --- a/vermouth/gmx/itp.py +++ b/vermouth/gmx/itp.py @@ -18,6 +18,7 @@ import copy import itertools +from vermouth.file_writer import deferred_open __all__ = ['write_molecule_itp', ] @@ -54,6 +55,27 @@ def _interaction_sorting_key(interaction): return (conditional, group) +def write_bond_params(interactions, itp_path, correspondence, max_length): + """ + Writes the [ bonds ] directive to file. + + interactions: list + list of bonded interactions to write to file + itp_path: str + name of external file to write + """ + with deferred_open(itp_path, "w") as itp_file: + itp_file.write('[ bonds ]\n') + for b_params in interactions: + atoms = ['{atom_idx:>{max_length[idx]}}' + .format(atom_idx=correspondence[x], + max_length=max_length) + for x in b_params.atoms] + parameters = ' '.join(str(x) for x in b_params.parameters) + comment = '' + + to_join = atoms + [parameters] + itp_file.write(' '.join(to_join) + comment + '\n') def write_molecule_itp(molecule, outfile, header=(), moltype=None, post_section_lines=None, pre_section_lines=None): @@ -194,6 +216,15 @@ def write_molecule_itp(molecule, outfile, header=(), moltype=None, # should be written under the [ dihedrals ] section of the ITP file. if name == 'impropers': name = 'dihedrals' + # el_bonds is a directive for elastic network bonds to be written out externally + if name == 'el_bonds': + outfile.write('#ifdef ELASTIC\n') + outfile.write('#include "en_bonds.itp"\n') + outfile.write('#endif\n\n') + write_bond_params(interactions, 'en_bonds.itp', + correspondence, max_length) + continue + outfile.write('[ {} ]\n'.format(name)) seen_sections.add(name) for line in pre_section_lines.get(name, []): diff --git a/vermouth/gmx/topology.py b/vermouth/gmx/topology.py index ccd537c3c..c837f18cd 100644 --- a/vermouth/gmx/topology.py +++ b/vermouth/gmx/topology.py @@ -158,6 +158,8 @@ def write_gmx_topology(system, _path = itp_paths['nonbond_params'] write_nonbond_params(system, _path, C6C12) include_string += f'\n #include "{_path}"\n' + + # Write the ITP files for the molecule types, and prepare writing the # [ molecules ] section of the top file. # * We write one ITP file for each different moltype in the system, the diff --git a/vermouth/processors/apply_rubber_band.py b/vermouth/processors/apply_rubber_band.py index 100ffc134..6f2b7e135 100644 --- a/vermouth/processors/apply_rubber_band.py +++ b/vermouth/processors/apply_rubber_band.py @@ -227,7 +227,7 @@ def apply_rubber_band(molecule, selector, lower_bound, upper_bound, decay_factor, decay_power, base_constant, minimum_force, - bond_type, domain_criterion, res_min_dist): + bond_type, domain_criterion, res_min_dist, eb_write): r""" Adds a rubber band elastic network to a molecule. @@ -295,6 +295,9 @@ def apply_rubber_band(molecule, selector, Minimum separation between two atoms for a bond to be kept. Bonds are kept is the separation is greater or equal to the value given. + eb_write: bool + if True, EN parameters get returned to be written out to an external file. + if False, EN parameters are written into the molecule's topology. """ selection = [] coordinates = [] @@ -341,6 +344,11 @@ def apply_rubber_band(molecule, selector, # Multiply the force constant by 0 if the nodes cannot be linked. constants *= can_be_linked distance_matrix = distance_matrix.round(5) # For compatibility with legacy + ebs = [] + if eb_write: + interaction_type = 'el_bonds' + else: + interaction_type = 'bonds' for from_idx, to_idx in zip(*np.triu_indices_from(constants)): # note the indices in the matrix are not anymore the idx of # the full molecule but the subset of nodes in selection @@ -350,12 +358,12 @@ def apply_rubber_band(molecule, selector, length = distance_matrix[from_idx, to_idx] if force_constant > minimum_force: molecule.add_interaction( - type_='bonds', + type_=interaction_type, atoms=(from_key, to_key), parameters=[bond_type, length, force_constant], - meta={'group': 'Rubber band'}, + meta={'group': 'Rubber band'} ) - + return ebs def always_true(*args, **kwargs): # pylint: disable=unused-argument """ @@ -493,7 +501,8 @@ def __init__(self, lower_bound, upper_bound, decay_factor, decay_power, selector=selectors.select_backbone, bond_type_variable='elastic_network_bond_type', res_min_dist_variable='elastic_network_res_min_dist', - domain_criterion=always_true): + domain_criterion=always_true, + write_out=False): super().__init__() self.lower_bound = lower_bound self.upper_bound = upper_bound @@ -507,6 +516,7 @@ def __init__(self, lower_bound, upper_bound, decay_factor, decay_power, self.domain_criterion = domain_criterion self.res_min_dist = res_min_dist self.res_min_dist_variable = res_min_dist_variable + self.write_out = write_out def run_molecule(self, molecule): # Choose the bond type. From high to low, the priority order is: @@ -535,5 +545,19 @@ def run_molecule(self, molecule): minimum_force=self.minimum_force, bond_type=bond_type, domain_criterion=self.domain_criterion, - res_min_dist=res_min_dist) + res_min_dist=res_min_dist, + eb_write=self.write_out) + return molecule + + def run_system(self, system): + """ + Process `system`. + + Parameters + ---------- + system: vermouth.system.System + The system to process. Is modified in-place. + """ + self.system = system + super().run_system(system) diff --git a/vermouth/tests/data/integration_tests/tier-1/EN_ext/aa.pdb b/vermouth/tests/data/integration_tests/tier-1/EN_ext/aa.pdb new file mode 100644 index 000000000..8f960de14 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/EN_ext/aa.pdb @@ -0,0 +1,788 @@ +HEADER HORMONE 01-JUL-09 3I40 +TITLE HUMAN INSULIN +COMPND MOL_ID: 1; +COMPND 2 MOLECULE: INSULIN A CHAIN; +COMPND 3 CHAIN: A; +COMPND 4 ENGINEERED: YES; +COMPND 5 MOL_ID: 2; +COMPND 6 MOLECULE: INSULIN B CHAIN; +COMPND 7 CHAIN: B; +COMPND 8 ENGINEERED: YES +SOURCE MOL_ID: 1; +SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; +SOURCE 3 ORGANISM_COMMON: HUMAN; +SOURCE 4 ORGANISM_TAXID: 9606; +SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; +SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; +SOURCE 7 MOL_ID: 2; +SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; +SOURCE 9 ORGANISM_COMMON: HUMAN; +SOURCE 10 ORGANISM_TAXID: 9606; +SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; +SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 +KEYWDS INSULIN, CARBOHYDRATE METABOLISM, CLEAVAGE ON PAIR OF BASIC RESIDUES, +KEYWDS 2 DIABETES MELLITUS, DISEASE MUTATION, DISULFIDE BOND, GLUCOSE +KEYWDS 3 METABOLISM, HORMONE, PHARMACEUTICAL, SECRETED +EXPDTA X-RAY DIFFRACTION +AUTHOR V.I.TIMOFEEV,V.V.BEZUGLOV,K.A.MIROSHNIKOV,R.N.CHUPROV-NETOCHIN, +AUTHOR 2 I.P.KURANOVA +REVDAT 2 05-MAY-10 3I40 1 JRNL +REVDAT 1 05-JAN-10 3I40 0 +JRNL AUTH V.I.TIMOFEEV,R.N.CHUPROV-NETOCHIN,V.R.SAMIGINA, +JRNL AUTH 2 V.V.BEZUGLOV,K.A.MIROSHNIKOV,I.P.KURANOVA +JRNL TITL X-RAY INVESTIGATION OF GENE-ENGINEERED HUMAN INSULIN +JRNL TITL 2 CRYSTALLIZED FROM A SOLUTION CONTAINING POLYSIALIC ACID. +JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 66 259 2010 +JRNL REFN ESSN 1744-3091 +JRNL PMID 20208155 +JRNL DOI 10.1107/S1744309110000461 +REMARK 2 +REMARK 2 RESOLUTION. 1.85 ANGSTROMS. +REMARK 3 +REMARK 3 REFINEMENT. +REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) +REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN +REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- +REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, +REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL +REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE +REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM +REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, +REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER +REMARK 3 : ZWART +REMARK 3 +REMARK 3 REFINEMENT TARGET : ML +REMARK 3 +REMARK 3 DATA USED IN REFINEMENT. +REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 +REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.52 +REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 +REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 +REMARK 3 NUMBER OF REFLECTIONS : 6640 +REMARK 3 +REMARK 3 FIT TO DATA USED IN REFINEMENT. +REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 +REMARK 3 R VALUE (WORKING SET) : 0.200 +REMARK 3 FREE R VALUE : 0.228 +REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 +REMARK 3 FREE R VALUE TEST SET COUNT : 316 +REMARK 3 +REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). +REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE +REMARK 3 1 31.5295 - 2.3309 1.00 3219 154 0.1910 0.2145 +REMARK 3 2 2.3309 - 1.8501 0.99 3105 162 0.2301 0.2627 +REMARK 3 +REMARK 3 BULK SOLVENT MODELLING. +REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL +REMARK 3 SOLVENT RADIUS : 1.11 +REMARK 3 SHRINKAGE RADIUS : 0.90 +REMARK 3 K_SOL : 0.35 +REMARK 3 B_SOL : 47.05 +REMARK 3 +REMARK 3 ERROR ESTIMATES. +REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 +REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.930 +REMARK 3 +REMARK 3 B VALUES. +REMARK 3 FROM WILSON PLOT (A**2) : 24.04 +REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.30 +REMARK 3 OVERALL ANISOTROPIC B VALUE. +REMARK 3 B11 (A**2) : NULL +REMARK 3 B22 (A**2) : NULL +REMARK 3 B33 (A**2) : NULL +REMARK 3 B12 (A**2) : NULL +REMARK 3 B13 (A**2) : NULL +REMARK 3 B23 (A**2) : NULL +REMARK 3 +REMARK 3 TWINNING INFORMATION. +REMARK 3 FRACTION: NULL +REMARK 3 OPERATOR: NULL +REMARK 3 +REMARK 3 DEVIATIONS FROM IDEAL VALUES. +REMARK 3 RMSD COUNT +REMARK 3 BOND : 0.005 423 +REMARK 3 ANGLE : 0.760 569 +REMARK 3 CHIRALITY : 0.068 62 +REMARK 3 PLANARITY : 0.002 73 +REMARK 3 DIHEDRAL : 17.205 141 +REMARK 3 +REMARK 3 TLS DETAILS +REMARK 3 NUMBER OF TLS GROUPS : NULL +REMARK 3 +REMARK 3 NCS DETAILS +REMARK 3 NUMBER OF NCS GROUPS : NULL +REMARK 3 +REMARK 3 OTHER REFINEMENT REMARKS: NULL +REMARK 4 +REMARK 4 3I40 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 +REMARK 100 +REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUL-09. +REMARK 100 THE RCSB ID CODE IS RCSB053935. +REMARK 200 +REMARK 200 EXPERIMENTAL DETAILS +REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION +REMARK 200 DATE OF DATA COLLECTION : 10-MAR-09 +REMARK 200 TEMPERATURE (KELVIN) : 100 +REMARK 200 PH : NULL +REMARK 200 NUMBER OF CRYSTALS USED : 1 +REMARK 200 +REMARK 200 SYNCHROTRON (Y/N) : N +REMARK 200 RADIATION SOURCE : ROTATING ANODE +REMARK 200 BEAMLINE : NULL +REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR +REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M +REMARK 200 WAVELENGTH OR RANGE (A) : NULL +REMARK 200 MONOCHROMATOR : NULL +REMARK 200 OPTICS : NULL +REMARK 200 +REMARK 200 DETECTOR TYPE : CCD +REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM +REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO +REMARK 200 DATA SCALING SOFTWARE : NULL +REMARK 200 +REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6677 +REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 +REMARK 200 RESOLUTION RANGE LOW (A) : 54.636 +REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL +REMARK 200 +REMARK 200 OVERALL. +REMARK 200 COMPLETENESS FOR RANGE (%) : NULL +REMARK 200 DATA REDUNDANCY : NULL +REMARK 200 R MERGE (I) : NULL +REMARK 200 R SYM (I) : NULL +REMARK 200 FOR THE DATA SET : NULL +REMARK 200 +REMARK 200 IN THE HIGHEST RESOLUTION SHELL. +REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL +REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL +REMARK 200 COMPLETENESS FOR SHELL (%) : NULL +REMARK 200 DATA REDUNDANCY IN SHELL : NULL +REMARK 200 R MERGE FOR SHELL (I) : NULL +REMARK 200 R SYM FOR SHELL (I) : NULL +REMARK 200 FOR SHELL : NULL +REMARK 200 +REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH +REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT +REMARK 200 SOFTWARE USED: NULL +REMARK 200 STARTING MODEL: PDB ENTRY 2G4M +REMARK 200 +REMARK 200 REMARK: NULL +REMARK 280 +REMARK 280 CRYSTAL +REMARK 280 SOLVENT CONTENT, VS (%): 62.90 +REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 +REMARK 280 +REMARK 280 CRYSTALLIZATION CONDITIONS: NULL +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY +REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 3 +REMARK 290 +REMARK 290 SYMOP SYMMETRY +REMARK 290 NNNMMM OPERATOR +REMARK 290 1555 X,Y,Z +REMARK 290 2555 -X+1/2,-Y,Z+1/2 +REMARK 290 3555 -X,Y+1/2,-Z+1/2 +REMARK 290 4555 X+1/2,-Y+1/2,-Z +REMARK 290 5555 Z,X,Y +REMARK 290 6555 Z+1/2,-X+1/2,-Y +REMARK 290 7555 -Z+1/2,-X,Y+1/2 +REMARK 290 8555 -Z,X+1/2,-Y+1/2 +REMARK 290 9555 Y,Z,X +REMARK 290 10555 -Y,Z+1/2,-X+1/2 +REMARK 290 11555 Y+1/2,-Z+1/2,-X +REMARK 290 12555 -Y+1/2,-Z,X+1/2 +REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 +REMARK 290 14555 -X,-Y+1/2,Z +REMARK 290 15555 -X+1/2,Y,-Z +REMARK 290 16555 X,-Y,-Z+1/2 +REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 +REMARK 290 18555 Z,-X,-Y+1/2 +REMARK 290 19555 -Z,-X+1/2,Y +REMARK 290 20555 -Z+1/2,X,-Y +REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 +REMARK 290 22555 -Y+1/2,Z,-X +REMARK 290 23555 Y,-Z,-X+1/2 +REMARK 290 24555 -Y,-Z+1/2,X +REMARK 290 +REMARK 290 WHERE NNN -> OPERATOR NUMBER +REMARK 290 MMM -> TRANSLATION VECTOR +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS +REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM +REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY +REMARK 290 RELATED MOLECULES. +REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 38.61000 +REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.61000 +REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.61000 +REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.61000 +REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.61000 +REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.61000 +REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 38.61000 +REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 38.61000 +REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 38.61000 +REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 38.61000 +REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 38.61000 +REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 38.61000 +REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 38.61000 +REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 38.61000 +REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 38.61000 +REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 38.61000 +REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 38.61000 +REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 38.61000 +REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 38.61000 +REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 38.61000 +REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 38.61000 +REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 38.61000 +REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 38.61000 +REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 38.61000 +REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 38.61000 +REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 38.61000 +REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 38.61000 +REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 38.61000 +REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 38.61000 +REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 38.61000 +REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 38.61000 +REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 38.61000 +REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 38.61000 +REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 38.61000 +REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 38.61000 +REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 38.61000 +REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 0.00000 +REMARK 290 +REMARK 290 REMARK: NULL +REMARK 300 +REMARK 300 BIOMOLECULE: 1 +REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM +REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN +REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON +REMARK 300 BURIED SURFACE AREA. +REMARK 350 +REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN +REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE +REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS +REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND +REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. +REMARK 350 +REMARK 350 BIOMOLECULE: 1 +REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC +REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC +REMARK 350 SOFTWARE USED: PISA +REMARK 350 TOTAL BURIED SURFACE AREA: 1520 ANGSTROM**2 +REMARK 350 SURFACE AREA OF THE COMPLEX: 3380 ANGSTROM**2 +REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL +REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B +REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 +REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 +REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 +REMARK 900 +REMARK 900 RELATED ENTRIES +REMARK 900 RELATED ID: 3I3Z RELATED DB: PDB +REMARK 999 +REMARK 999 SEQUENCE +REMARK 999 THE CONFLICT OF THE SEQUENCE MAY DUE TO ARTIFACT. +DBREF 3I40 A 1 21 UNP P01308 INS_HUMAN 90 110 +DBREF 3I40 B 1 30 UNP P01308 INS_HUMAN 25 54 +SEQADV 3I40 ALA B 30 UNP P01308 THR 54 SEE REMARK 999 +SEQRES 1 A 21 GLY ILE VAL GLU GLN CYS CYS THR SER ILE CYS SER LEU +SEQRES 2 A 21 TYR GLN LEU GLU ASN TYR CYS ASN +SEQRES 1 B 30 PHE VAL ASN GLN HIS LEU CYS GLY SER HIS LEU VAL GLU +SEQRES 2 B 30 ALA LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE PHE TYR +SEQRES 3 B 30 THR PRO LYS ALA +FORMUL 3 HOH *35(H2 O) +HELIX 1 1 GLY A 1 CYS A 7 1 7 +HELIX 2 2 SER A 12 ASN A 18 1 7 +HELIX 3 3 GLY B 8 GLY B 20 1 13 +HELIX 4 4 GLU B 21 GLY B 23 5 3 +SSBOND 1 CYS A 6 CYS A 11 1555 1555 2.03 +SSBOND 2 CYS A 7 CYS B 7 1555 1555 2.04 +SSBOND 3 CYS A 20 CYS B 19 1555 1555 2.04 +CRYST1 77.220 77.220 77.220 90.00 90.00 90.00 I 21 3 24 +ORIGX1 1.000000 0.000000 0.000000 0.00000 +ORIGX2 0.000000 1.000000 0.000000 0.00000 +ORIGX3 0.000000 0.000000 1.000000 0.00000 +SCALE1 0.012950 0.000000 0.000000 0.00000 +SCALE2 0.000000 0.012950 0.000000 0.00000 +SCALE3 0.000000 0.000000 0.012950 0.00000 +ATOM 1 N GLY A 1 -27.279 6.238 -12.314 1.00 45.01 N +ATOM 2 CA GLY A 1 -26.249 6.028 -11.313 1.00 43.47 C +ATOM 3 C GLY A 1 -25.582 4.677 -11.471 1.00 34.37 C +ATOM 4 O GLY A 1 -25.731 4.023 -12.501 1.00 30.09 O +ATOM 5 N ILE A 2 -24.853 4.248 -10.446 1.00 32.71 N +ATOM 6 CA ILE A 2 -24.070 3.023 -10.550 1.00 22.60 C +ATOM 7 C ILE A 2 -24.915 1.786 -10.840 1.00 23.32 C +ATOM 8 O ILE A 2 -24.469 0.865 -11.529 1.00 26.36 O +ATOM 9 CB ILE A 2 -23.208 2.791 -9.302 1.00 28.24 C +ATOM 10 CG1 ILE A 2 -22.249 1.620 -9.538 1.00 25.03 C +ATOM 11 CG2 ILE A 2 -24.090 2.579 -8.068 1.00 32.70 C +ATOM 12 CD1 ILE A 2 -21.209 1.479 -8.457 1.00 30.60 C +ATOM 13 N VAL A 3 -26.137 1.755 -10.324 1.00 27.13 N +ATOM 14 CA VAL A 3 -26.993 0.599 -10.563 1.00 30.10 C +ATOM 15 C VAL A 3 -27.324 0.471 -12.049 1.00 32.71 C +ATOM 16 O VAL A 3 -27.258 -0.617 -12.621 1.00 28.83 O +ATOM 17 CB VAL A 3 -28.284 0.657 -9.740 1.00 30.51 C +ATOM 18 CG1 VAL A 3 -29.194 -0.497 -10.127 1.00 35.07 C +ATOM 19 CG2 VAL A 3 -27.956 0.613 -8.242 1.00 27.53 C +ATOM 20 N GLU A 4 -27.669 1.596 -12.667 1.00 34.97 N +ATOM 21 CA GLU A 4 -28.001 1.627 -14.086 1.00 31.24 C +ATOM 22 C GLU A 4 -26.797 1.224 -14.927 1.00 32.52 C +ATOM 23 O GLU A 4 -26.933 0.517 -15.924 1.00 31.47 O +ATOM 24 CB GLU A 4 -28.474 3.027 -14.485 1.00 38.19 C +ATOM 25 CG GLU A 4 -29.829 3.420 -13.908 1.00 61.51 C +ATOM 26 CD GLU A 4 -29.832 3.535 -12.387 1.00 66.16 C +ATOM 27 OE1 GLU A 4 -28.868 4.094 -11.814 1.00 42.60 O +ATOM 28 OE2 GLU A 4 -30.812 3.071 -11.762 1.00 67.86 O +ATOM 29 N GLN A 5 -25.615 1.664 -14.508 1.00 28.29 N +ATOM 30 CA GLN A 5 -24.393 1.410 -15.266 1.00 31.01 C +ATOM 31 C GLN A 5 -23.776 0.028 -15.056 1.00 39.69 C +ATOM 32 O GLN A 5 -23.149 -0.511 -15.967 1.00 26.39 O +ATOM 33 CB GLN A 5 -23.349 2.492 -14.974 1.00 25.23 C +ATOM 34 CG GLN A 5 -23.818 3.887 -15.346 1.00 38.13 C +ATOM 35 CD GLN A 5 -24.535 3.921 -16.693 1.00 53.62 C +ATOM 36 OE1 GLN A 5 -24.074 3.334 -17.674 1.00 38.85 O +ATOM 37 NE2 GLN A 5 -25.671 4.609 -16.741 1.00 42.57 N +ATOM 38 N CYS A 6 -23.940 -0.551 -13.868 1.00 22.46 N +ATOM 39 CA CYS A 6 -23.214 -1.776 -13.549 1.00 20.37 C +ATOM 40 C CYS A 6 -24.114 -2.963 -13.225 1.00 18.21 C +ATOM 41 O CYS A 6 -23.677 -4.107 -13.293 1.00 21.83 O +ATOM 42 CB CYS A 6 -22.235 -1.524 -12.396 1.00 22.32 C +ATOM 43 SG CYS A 6 -20.756 -0.602 -12.893 1.00 27.82 S +ATOM 44 N CYS A 7 -25.359 -2.685 -12.860 1.00 22.16 N +ATOM 45 CA CYS A 7 -26.307 -3.744 -12.520 1.00 21.25 C +ATOM 46 C CYS A 7 -27.245 -4.032 -13.690 1.00 31.44 C +ATOM 47 O CYS A 7 -27.307 -5.155 -14.190 1.00 24.09 O +ATOM 48 CB CYS A 7 -27.119 -3.351 -11.286 1.00 22.97 C +ATOM 49 SG CYS A 7 -28.355 -4.584 -10.791 1.00 28.27 S +ATOM 50 N THR A 8 -27.967 -3.001 -14.122 1.00 29.15 N +ATOM 51 CA THR A 8 -28.901 -3.121 -15.236 1.00 29.59 C +ATOM 52 C THR A 8 -28.147 -3.334 -16.542 1.00 34.52 C +ATOM 53 O THR A 8 -28.647 -3.986 -17.454 1.00 38.61 O +ATOM 54 CB THR A 8 -29.780 -1.868 -15.371 1.00 31.24 C +ATOM 55 OG1 THR A 8 -30.023 -1.303 -14.080 1.00 41.12 O +ATOM 56 CG2 THR A 8 -31.100 -2.218 -16.029 1.00 51.07 C +ATOM 57 N SER A 9 -26.948 -2.769 -16.630 1.00 26.15 N +ATOM 58 CA SER A 9 -26.064 -3.019 -17.765 1.00 21.41 C +ATOM 59 C SER A 9 -24.699 -3.529 -17.309 1.00 32.36 C +ATOM 60 O SER A 9 -24.419 -3.594 -16.111 1.00 29.40 O +ATOM 61 CB SER A 9 -25.910 -1.765 -18.626 1.00 32.53 C +ATOM 62 OG SER A 9 -25.465 -0.670 -17.851 1.00 47.07 O +ATOM 63 N ILE A 10 -23.849 -3.891 -18.261 1.00 24.43 N +ATOM 64 CA ILE A 10 -22.562 -4.492 -17.924 1.00 24.22 C +ATOM 65 C ILE A 10 -21.591 -3.454 -17.367 1.00 30.49 C +ATOM 66 O ILE A 10 -21.420 -2.380 -17.934 1.00 26.28 O +ATOM 67 CB ILE A 10 -21.942 -5.216 -19.128 1.00 26.99 C +ATOM 68 CG1 ILE A 10 -22.880 -6.328 -19.595 1.00 26.49 C +ATOM 69 CG2 ILE A 10 -20.577 -5.790 -18.770 1.00 25.10 C +ATOM 70 CD1 ILE A 10 -22.302 -7.179 -20.689 1.00 44.31 C +ATOM 71 N CYS A 11 -20.972 -3.790 -16.240 1.00 28.14 N +ATOM 72 CA CYS A 11 -20.088 -2.876 -15.534 1.00 25.92 C +ATOM 73 C CYS A 11 -18.752 -2.779 -16.258 1.00 36.06 C +ATOM 74 O CYS A 11 -18.491 -3.524 -17.204 1.00 27.25 O +ATOM 75 CB CYS A 11 -19.867 -3.387 -14.106 1.00 23.76 C +ATOM 76 SG CYS A 11 -19.406 -2.114 -12.908 1.00 28.09 S +ATOM 77 N SER A 12 -17.902 -1.865 -15.807 1.00 25.78 N +ATOM 78 CA SER A 12 -16.554 -1.767 -16.349 1.00 22.91 C +ATOM 79 C SER A 12 -15.634 -1.220 -15.281 1.00 19.20 C +ATOM 80 O SER A 12 -16.076 -0.508 -14.375 1.00 18.62 O +ATOM 81 CB SER A 12 -16.530 -0.845 -17.559 1.00 24.50 C +ATOM 82 OG SER A 12 -16.681 0.502 -17.157 1.00 24.75 O +ATOM 83 N LEU A 13 -14.346 -1.528 -15.392 1.00 22.17 N +ATOM 84 CA LEU A 13 -13.378 -1.013 -14.426 1.00 19.72 C +ATOM 85 C LEU A 13 -13.412 0.508 -14.438 1.00 22.22 C +ATOM 86 O LEU A 13 -13.329 1.158 -13.393 1.00 17.29 O +ATOM 87 CB LEU A 13 -11.971 -1.517 -14.751 1.00 19.22 C +ATOM 88 CG LEU A 13 -10.860 -0.998 -13.840 1.00 17.99 C +ATOM 89 CD1 LEU A 13 -11.104 -1.386 -12.388 1.00 18.06 C +ATOM 90 CD2 LEU A 13 -9.522 -1.530 -14.308 1.00 15.25 C +ATOM 91 N TYR A 14 -13.550 1.075 -15.632 1.00 19.94 N +ATOM 92 CA TYR A 14 -13.559 2.521 -15.774 1.00 22.72 C +ATOM 93 C TYR A 14 -14.638 3.140 -14.893 1.00 22.64 C +ATOM 94 O TYR A 14 -14.391 4.094 -14.152 1.00 25.33 O +ATOM 95 CB TYR A 14 -13.771 2.911 -17.239 0.50 27.81 C +ATOM 97 CG TYR A 14 -13.608 4.388 -17.494 0.50 28.31 C +ATOM 99 CD1 TYR A 14 -12.442 4.893 -18.059 0.50 23.25 C +ATOM 101 CD2 TYR A 14 -14.614 5.282 -17.153 0.50 28.36 C +ATOM 103 CE1 TYR A 14 -12.289 6.252 -18.283 0.50 27.32 C +ATOM 105 CE2 TYR A 14 -14.472 6.636 -17.372 0.50 29.32 C +ATOM 107 CZ TYR A 14 -13.311 7.117 -17.938 0.50 29.06 C +ATOM 109 OH TYR A 14 -13.179 8.469 -18.153 0.50 33.01 O +ATOM 111 N GLN A 15 -15.837 2.584 -14.969 1.00 21.27 N +ATOM 112 CA GLN A 15 -16.962 3.129 -14.222 1.00 21.51 C +ATOM 113 C GLN A 15 -16.837 2.882 -12.722 1.00 17.30 C +ATOM 114 O GLN A 15 -17.121 3.764 -11.917 1.00 20.82 O +ATOM 115 CB GLN A 15 -18.275 2.561 -14.758 1.00 25.25 C +ATOM 116 CG GLN A 15 -18.527 2.905 -16.214 1.00 32.75 C +ATOM 117 CD GLN A 15 -19.997 3.039 -16.527 1.00 55.05 C +ATOM 118 OE1 GLN A 15 -20.680 3.914 -15.987 1.00 53.01 O +ATOM 119 NE2 GLN A 15 -20.497 2.177 -17.410 1.00 50.66 N +ATOM 120 N LEU A 16 -16.399 1.687 -12.346 1.00 15.37 N +ATOM 121 CA LEU A 16 -16.236 1.380 -10.930 1.00 17.02 C +ATOM 122 C LEU A 16 -15.301 2.382 -10.273 1.00 16.55 C +ATOM 123 O LEU A 16 -15.565 2.868 -9.172 1.00 19.70 O +ATOM 124 CB LEU A 16 -15.703 -0.037 -10.742 1.00 24.64 C +ATOM 125 CG LEU A 16 -16.709 -1.151 -11.013 1.00 24.23 C +ATOM 126 CD1 LEU A 16 -16.007 -2.496 -11.058 1.00 21.90 C +ATOM 127 CD2 LEU A 16 -17.786 -1.124 -9.936 1.00 18.48 C +ATOM 128 N GLU A 17 -14.199 2.703 -10.950 1.00 17.86 N +ATOM 129 CA GLU A 17 -13.219 3.608 -10.365 1.00 19.38 C +ATOM 130 C GLU A 17 -13.763 5.026 -10.180 1.00 18.73 C +ATOM 131 O GLU A 17 -13.259 5.782 -9.351 1.00 22.43 O +ATOM 132 CB GLU A 17 -11.910 3.598 -11.155 1.00 20.40 C +ATOM 133 CG GLU A 17 -11.090 2.343 -10.898 1.00 20.17 C +ATOM 134 CD GLU A 17 -9.623 2.514 -11.240 1.00 22.14 C +ATOM 135 OE1 GLU A 17 -9.301 3.347 -12.110 1.00 22.42 O +ATOM 136 OE2 GLU A 17 -8.792 1.805 -10.640 1.00 27.73 O +ATOM 137 N ASN A 18 -14.799 5.374 -10.932 1.00 20.29 N +ATOM 138 CA ASN A 18 -15.480 6.657 -10.735 1.00 20.00 C +ATOM 139 C ASN A 18 -16.080 6.766 -9.334 1.00 26.36 C +ATOM 140 O ASN A 18 -16.469 7.849 -8.890 1.00 28.46 O +ATOM 141 CB ASN A 18 -16.587 6.839 -11.774 1.00 21.66 C +ATOM 142 CG ASN A 18 -16.061 7.344 -13.113 1.00 25.89 C +ATOM 143 OD1 ASN A 18 -15.007 7.974 -13.180 1.00 32.32 O +ATOM 144 ND2 ASN A 18 -16.802 7.070 -14.180 1.00 38.57 N +ATOM 145 N TYR A 19 -16.163 5.640 -8.638 1.00 20.84 N +ATOM 146 CA TYR A 19 -16.803 5.618 -7.327 1.00 18.56 C +ATOM 147 C TYR A 19 -15.822 5.394 -6.180 1.00 23.20 C +ATOM 148 O TYR A 19 -16.223 5.337 -5.018 1.00 27.54 O +ATOM 149 CB TYR A 19 -17.945 4.599 -7.298 1.00 20.89 C +ATOM 150 CG TYR A 19 -19.068 4.966 -8.236 1.00 21.62 C +ATOM 151 CD1 TYR A 19 -19.115 4.453 -9.521 1.00 23.43 C +ATOM 152 CD2 TYR A 19 -20.066 5.848 -7.844 1.00 26.68 C +ATOM 153 CE1 TYR A 19 -20.126 4.796 -10.385 1.00 24.39 C +ATOM 154 CE2 TYR A 19 -21.082 6.200 -8.708 1.00 31.02 C +ATOM 155 CZ TYR A 19 -21.104 5.672 -9.979 1.00 28.36 C +ATOM 156 OH TYR A 19 -22.114 6.009 -10.853 1.00 42.08 O +ATOM 157 N CYS A 20 -14.534 5.281 -6.499 1.00 21.90 N +ATOM 158 CA CYS A 20 -13.510 5.251 -5.459 1.00 19.66 C +ATOM 159 C CYS A 20 -13.334 6.645 -4.882 1.00 28.69 C +ATOM 160 O CYS A 20 -13.526 7.639 -5.585 1.00 30.53 O +ATOM 161 CB CYS A 20 -12.169 4.783 -6.021 1.00 22.84 C +ATOM 162 SG CYS A 20 -12.209 3.187 -6.829 1.00 22.45 S +ATOM 163 N ASN A 21 -12.955 6.716 -3.609 1.00 26.51 N +ATOM 164 CA ASN A 21 -12.630 7.993 -2.976 1.00 36.60 C +ATOM 165 C ASN A 21 -11.279 8.511 -3.448 1.00 35.58 C +ATOM 166 O ASN A 21 -10.515 7.790 -4.091 1.00 36.84 O +ATOM 167 CB ASN A 21 -12.615 7.863 -1.450 1.00 34.89 C +ATOM 168 CG ASN A 21 -13.978 7.548 -0.878 1.00 33.46 C +ATOM 169 OD1 ASN A 21 -14.107 6.726 0.029 1.00 48.60 O +ATOM 170 ND2 ASN A 21 -15.008 8.198 -1.408 1.00 39.53 N +ATOM 171 OXT ASN A 21 -10.922 9.659 -3.189 1.00 58.00 O +TER 172 ASN A 21 +ATOM 173 N PHE B 1 -13.174 -9.740 -13.251 1.00 44.56 N +ATOM 174 CA PHE B 1 -14.387 -9.892 -12.452 1.00 53.84 C +ATOM 175 C PHE B 1 -15.310 -8.684 -12.590 1.00 44.51 C +ATOM 176 O PHE B 1 -16.451 -8.715 -12.133 1.00 40.17 O +ATOM 177 CB PHE B 1 -14.042 -10.126 -10.973 1.00 47.36 C +ATOM 178 CG PHE B 1 -13.222 -9.024 -10.356 1.00 43.05 C +ATOM 179 CD1 PHE B 1 -13.816 -8.050 -9.571 1.00 39.13 C +ATOM 180 CD2 PHE B 1 -11.854 -8.964 -10.565 1.00 48.11 C +ATOM 181 CE1 PHE B 1 -13.059 -7.037 -9.008 1.00 29.34 C +ATOM 182 CE2 PHE B 1 -11.093 -7.959 -10.002 1.00 34.97 C +ATOM 183 CZ PHE B 1 -11.696 -6.993 -9.224 1.00 36.24 C +ATOM 184 N VAL B 2 -14.819 -7.623 -13.228 1.00 27.44 N +ATOM 185 CA VAL B 2 -15.568 -6.367 -13.273 1.00 25.65 C +ATOM 186 C VAL B 2 -16.402 -6.197 -14.541 1.00 30.55 C +ATOM 187 O VAL B 2 -17.249 -5.306 -14.628 1.00 30.98 O +ATOM 188 CB VAL B 2 -14.633 -5.163 -13.114 1.00 32.50 C +ATOM 189 CG1 VAL B 2 -14.056 -5.139 -11.705 1.00 29.74 C +ATOM 190 CG2 VAL B 2 -13.519 -5.227 -14.141 1.00 45.24 C +ATOM 191 N ASN B 3 -16.158 -7.045 -15.528 1.00 28.57 N +ATOM 192 CA ASN B 3 -16.844 -6.904 -16.806 1.00 31.00 C +ATOM 193 C ASN B 3 -18.072 -7.800 -16.928 1.00 29.49 C +ATOM 194 O ASN B 3 -18.115 -8.720 -17.743 1.00 28.57 O +ATOM 195 CB ASN B 3 -15.854 -7.122 -17.946 1.00 31.67 C +ATOM 196 CG ASN B 3 -14.703 -6.139 -17.888 1.00 35.45 C +ATOM 197 OD1 ASN B 3 -13.561 -6.507 -17.600 1.00 38.37 O +ATOM 198 ND2 ASN B 3 -15.009 -4.871 -18.113 1.00 23.34 N +ATOM 199 N GLN B 4 -19.073 -7.514 -16.099 1.00 31.90 N +ATOM 200 CA GLN B 4 -20.313 -8.287 -16.082 1.00 28.96 C +ATOM 201 C GLN B 4 -21.397 -7.521 -15.328 1.00 23.12 C +ATOM 202 O GLN B 4 -21.154 -6.432 -14.812 1.00 26.67 O +ATOM 203 CB GLN B 4 -20.079 -9.648 -15.425 1.00 33.50 C +ATOM 204 CG GLN B 4 -19.608 -9.556 -13.987 1.00 31.03 C +ATOM 205 CD GLN B 4 -19.344 -10.918 -13.379 1.00 54.72 C +ATOM 206 OE1 GLN B 4 -20.210 -11.794 -13.390 1.00 51.79 O +ATOM 207 NE2 GLN B 4 -18.144 -11.105 -12.840 1.00 41.70 N +ATOM 208 N HIS B 5 -22.599 -8.080 -15.281 1.00 25.17 N +ATOM 209 CA HIS B 5 -23.666 -7.471 -14.503 1.00 26.87 C +ATOM 210 C HIS B 5 -23.358 -7.685 -13.035 1.00 26.33 C +ATOM 211 O HIS B 5 -23.193 -8.822 -12.595 1.00 25.34 O +ATOM 212 CB HIS B 5 -25.013 -8.109 -14.834 1.00 24.65 C +ATOM 213 CG HIS B 5 -25.462 -7.871 -16.239 1.00 27.43 C +ATOM 214 ND1 HIS B 5 -26.235 -6.787 -16.598 1.00 29.87 N +ATOM 215 CD2 HIS B 5 -25.241 -8.570 -17.377 1.00 27.84 C +ATOM 216 CE1 HIS B 5 -26.478 -6.833 -17.896 1.00 24.52 C +ATOM 217 NE2 HIS B 5 -25.885 -7.905 -18.393 1.00 35.03 N +ATOM 218 N LEU B 6 -23.267 -6.592 -12.287 1.00 22.69 N +ATOM 219 CA LEU B 6 -22.974 -6.660 -10.862 1.00 21.06 C +ATOM 220 C LEU B 6 -24.052 -5.932 -10.079 1.00 21.50 C +ATOM 221 O LEU B 6 -24.197 -4.715 -10.194 1.00 22.66 O +ATOM 222 CB LEU B 6 -21.612 -6.034 -10.568 1.00 20.56 C +ATOM 223 CG LEU B 6 -20.418 -6.665 -11.281 1.00 20.16 C +ATOM 224 CD1 LEU B 6 -19.190 -5.786 -11.103 1.00 20.54 C +ATOM 225 CD2 LEU B 6 -20.155 -8.064 -10.763 1.00 25.22 C +ATOM 226 N CYS B 7 -24.800 -6.679 -9.273 1.00 20.58 N +ATOM 227 CA CYS B 7 -25.899 -6.104 -8.513 1.00 22.46 C +ATOM 228 C CYS B 7 -25.754 -6.421 -7.034 1.00 22.72 C +ATOM 229 O CYS B 7 -25.231 -7.471 -6.665 1.00 21.90 O +ATOM 230 CB CYS B 7 -27.236 -6.664 -9.009 1.00 28.16 C +ATOM 231 SG CYS B 7 -27.554 -6.459 -10.788 1.00 29.45 S +ATOM 232 N GLY B 8 -26.229 -5.514 -6.191 1.00 21.36 N +ATOM 233 CA GLY B 8 -26.233 -5.745 -4.759 1.00 22.98 C +ATOM 234 C GLY B 8 -24.859 -6.051 -4.209 1.00 20.91 C +ATOM 235 O GLY B 8 -23.911 -5.316 -4.465 1.00 23.25 O +ATOM 236 N SER B 9 -24.741 -7.136 -3.447 1.00 18.12 N +ATOM 237 CA SER B 9 -23.484 -7.444 -2.778 1.00 15.90 C +ATOM 238 C SER B 9 -22.360 -7.702 -3.780 1.00 18.45 C +ATOM 239 O SER B 9 -21.183 -7.509 -3.473 1.00 17.21 O +ATOM 240 CB SER B 9 -23.648 -8.663 -1.863 1.00 19.34 C +ATOM 241 OG SER B 9 -23.919 -9.813 -2.638 1.00 20.35 O +ATOM 242 N HIS B 10 -22.730 -8.151 -4.972 1.00 14.91 N +ATOM 243 CA HIS B 10 -21.764 -8.403 -6.039 1.00 17.86 C +ATOM 244 C HIS B 10 -21.093 -7.097 -6.470 1.00 18.59 C +ATOM 245 O HIS B 10 -19.891 -7.055 -6.725 1.00 17.96 O +ATOM 246 CB HIS B 10 -22.471 -9.047 -7.236 1.00 18.56 C +ATOM 247 CG HIS B 10 -23.081 -10.384 -6.933 1.00 23.08 C +ATOM 248 ND1 HIS B 10 -23.461 -11.269 -7.919 1.00 27.72 N +ATOM 249 CD2 HIS B 10 -23.366 -10.990 -5.755 1.00 23.69 C +ATOM 250 CE1 HIS B 10 -23.951 -12.364 -7.363 1.00 29.56 C +ATOM 251 NE2 HIS B 10 -23.906 -12.220 -6.050 1.00 22.03 N +ATOM 252 N LEU B 11 -21.886 -6.037 -6.550 1.00 16.34 N +ATOM 253 CA LEU B 11 -21.398 -4.713 -6.938 1.00 16.50 C +ATOM 254 C LEU B 11 -20.523 -4.120 -5.847 1.00 19.44 C +ATOM 255 O LEU B 11 -19.446 -3.585 -6.105 1.00 17.25 O +ATOM 256 CB LEU B 11 -22.588 -3.788 -7.211 1.00 16.97 C +ATOM 257 CG LEU B 11 -22.268 -2.390 -7.735 1.00 22.79 C +ATOM 258 CD1 LEU B 11 -21.211 -2.486 -8.812 1.00 17.51 C +ATOM 259 CD2 LEU B 11 -23.529 -1.754 -8.277 1.00 22.41 C +ATOM 260 N VAL B 12 -20.990 -4.218 -4.610 1.00 15.40 N +ATOM 261 CA VAL B 12 -20.242 -3.690 -3.490 1.00 13.81 C +ATOM 262 C VAL B 12 -18.902 -4.422 -3.332 1.00 15.23 C +ATOM 263 O VAL B 12 -17.879 -3.825 -2.988 1.00 14.98 O +ATOM 264 CB VAL B 12 -21.096 -3.776 -2.212 1.00 24.43 C +ATOM 265 CG1 VAL B 12 -20.252 -3.609 -1.029 1.00 30.29 C +ATOM 266 CG2 VAL B 12 -22.169 -2.694 -2.241 1.00 21.29 C +ATOM 267 N GLU B 13 -18.912 -5.721 -3.589 1.00 14.50 N +ATOM 268 CA GLU B 13 -17.695 -6.515 -3.515 1.00 14.19 C +ATOM 269 C GLU B 13 -16.682 -6.056 -4.574 1.00 15.30 C +ATOM 270 O GLU B 13 -15.481 -5.936 -4.304 1.00 16.00 O +ATOM 271 CB GLU B 13 -18.046 -7.986 -3.712 1.00 22.91 C +ATOM 272 CG GLU B 13 -16.884 -8.875 -4.073 1.00 31.68 C +ATOM 273 CD GLU B 13 -17.296 -10.336 -4.139 1.00 35.29 C +ATOM 274 OE1 GLU B 13 -17.726 -10.873 -3.092 1.00 24.65 O +ATOM 275 OE2 GLU B 13 -17.204 -10.932 -5.236 1.00 35.79 O +ATOM 276 N ALA B 14 -17.166 -5.811 -5.782 1.00 16.94 N +ATOM 277 CA ALA B 14 -16.298 -5.308 -6.856 1.00 19.02 C +ATOM 278 C ALA B 14 -15.701 -3.941 -6.523 1.00 17.95 C +ATOM 279 O ALA B 14 -14.507 -3.704 -6.731 1.00 16.40 O +ATOM 280 CB ALA B 14 -17.065 -5.240 -8.157 1.00 19.13 C +ATOM 281 N LEU B 15 -16.536 -3.036 -6.021 1.00 15.53 N +ATOM 282 CA LEU B 15 -16.066 -1.724 -5.592 1.00 13.58 C +ATOM 283 C LEU B 15 -14.977 -1.846 -4.540 1.00 20.33 C +ATOM 284 O LEU B 15 -13.957 -1.159 -4.594 1.00 17.96 O +ATOM 285 CB LEU B 15 -17.228 -0.890 -5.054 1.00 17.56 C +ATOM 286 CG LEU B 15 -18.132 -0.253 -6.108 1.00 19.95 C +ATOM 287 CD1 LEU B 15 -19.434 0.217 -5.476 1.00 19.70 C +ATOM 288 CD2 LEU B 15 -17.420 0.908 -6.806 1.00 19.43 C +ATOM 289 N TYR B 16 -15.196 -2.733 -3.580 1.00 16.41 N +ATOM 290 CA TYR B 16 -14.214 -2.982 -2.528 1.00 14.22 C +ATOM 291 C TYR B 16 -12.884 -3.467 -3.093 1.00 18.76 C +ATOM 292 O TYR B 16 -11.823 -2.978 -2.708 1.00 14.92 O +ATOM 293 CB TYR B 16 -14.766 -4.015 -1.551 1.00 13.58 C +ATOM 294 CG TYR B 16 -13.748 -4.582 -0.595 1.00 15.85 C +ATOM 295 CD1 TYR B 16 -13.213 -3.811 0.431 1.00 19.91 C +ATOM 296 CD2 TYR B 16 -13.338 -5.909 -0.707 1.00 14.31 C +ATOM 297 CE1 TYR B 16 -12.290 -4.347 1.318 1.00 18.93 C +ATOM 298 CE2 TYR B 16 -12.419 -6.445 0.163 1.00 16.89 C +ATOM 299 CZ TYR B 16 -11.899 -5.665 1.173 1.00 19.03 C +ATOM 300 OH TYR B 16 -10.991 -6.225 2.037 1.00 19.26 O +ATOM 301 N LEU B 17 -12.941 -4.437 -4.002 1.00 17.26 N +ATOM 302 CA LEU B 17 -11.725 -4.998 -4.583 1.00 17.15 C +ATOM 303 C LEU B 17 -10.983 -3.979 -5.439 1.00 20.48 C +ATOM 304 O LEU B 17 -9.751 -3.889 -5.407 1.00 20.37 O +ATOM 305 CB LEU B 17 -12.060 -6.221 -5.428 1.00 16.44 C +ATOM 306 CG LEU B 17 -12.491 -7.468 -4.651 1.00 17.44 C +ATOM 307 CD1 LEU B 17 -12.867 -8.590 -5.593 1.00 22.58 C +ATOM 308 CD2 LEU B 17 -11.383 -7.898 -3.717 1.00 22.13 C +ATOM 309 N VAL B 18 -11.738 -3.226 -6.224 1.00 18.15 N +ATOM 310 CA VAL B 18 -11.150 -2.270 -7.151 1.00 18.50 C +ATOM 311 C VAL B 18 -10.557 -1.063 -6.431 1.00 22.53 C +ATOM 312 O VAL B 18 -9.454 -0.628 -6.747 1.00 21.63 O +ATOM 313 CB VAL B 18 -12.188 -1.824 -8.207 1.00 19.51 C +ATOM 314 CG1 VAL B 18 -11.714 -0.594 -8.955 1.00 28.07 C +ATOM 315 CG2 VAL B 18 -12.468 -2.973 -9.165 1.00 23.98 C +ATOM 316 N CYS B 19 -11.268 -0.548 -5.433 1.00 19.45 N +ATOM 317 CA CYS B 19 -10.874 0.709 -4.803 1.00 21.28 C +ATOM 318 C CYS B 19 -9.819 0.588 -3.702 1.00 26.60 C +ATOM 319 O CYS B 19 -9.167 1.576 -3.355 1.00 25.82 O +ATOM 320 CB CYS B 19 -12.102 1.455 -4.285 1.00 20.90 C +ATOM 321 SG CYS B 19 -13.231 1.932 -5.593 1.00 21.21 S +ATOM 322 N GLY B 20 -9.653 -0.608 -3.150 1.00 25.20 N +ATOM 323 CA GLY B 20 -8.606 -0.825 -2.167 1.00 33.63 C +ATOM 324 C GLY B 20 -8.661 0.162 -1.014 1.00 39.29 C +ATOM 325 O GLY B 20 -9.737 0.464 -0.501 1.00 27.87 O +ATOM 326 N GLU B 21 -7.507 0.678 -0.599 1.00 30.38 N +ATOM 327 CA GLU B 21 -7.474 1.534 0.591 1.00 34.13 C +ATOM 328 C GLU B 21 -8.014 2.944 0.351 1.00 23.63 C +ATOM 329 O GLU B 21 -8.123 3.737 1.283 1.00 35.45 O +ATOM 330 CB GLU B 21 -6.075 1.569 1.220 1.00 45.91 C +ATOM 331 CG GLU B 21 -5.015 2.280 0.401 1.00 57.50 C +ATOM 332 CD GLU B 21 -3.631 2.179 1.034 1.00 75.22 C +ATOM 333 OE1 GLU B 21 -2.707 2.876 0.563 1.00 79.46 O +ATOM 334 OE2 GLU B 21 -3.470 1.401 2.002 1.00 57.31 O +ATOM 335 N ARG B 22 -8.356 3.251 -0.897 1.00 27.41 N +ATOM 336 CA ARG B 22 -9.040 4.498 -1.213 1.00 28.81 C +ATOM 337 C ARG B 22 -10.456 4.461 -0.645 1.00 33.76 C +ATOM 338 O ARG B 22 -11.008 5.480 -0.235 1.00 31.35 O +ATOM 339 CB ARG B 22 -9.130 4.700 -2.726 1.00 30.48 C +ATOM 340 CG ARG B 22 -7.876 5.228 -3.400 1.00 38.41 C +ATOM 341 CD ARG B 22 -8.072 5.288 -4.922 1.00 44.34 C +ATOM 342 NE ARG B 22 -8.003 3.963 -5.546 1.00 61.53 N +ATOM 343 CZ ARG B 22 -8.246 3.711 -6.833 1.00 56.00 C +ATOM 344 NH1 ARG B 22 -8.151 2.467 -7.288 1.00 37.21 N +ATOM 345 NH2 ARG B 22 -8.588 4.690 -7.664 1.00 33.73 N +ATOM 346 N GLY B 23 -11.048 3.276 -0.627 1.00 23.72 N +ATOM 347 CA GLY B 23 -12.442 3.151 -0.243 1.00 25.22 C +ATOM 348 C GLY B 23 -13.323 3.633 -1.376 1.00 26.84 C +ATOM 349 O GLY B 23 -12.832 3.954 -2.460 1.00 20.71 O +ATOM 350 N PHE B 24 -14.625 3.700 -1.132 1.00 18.98 N +ATOM 351 CA PHE B 24 -15.558 4.055 -2.188 1.00 17.55 C +ATOM 352 C PHE B 24 -16.875 4.561 -1.614 1.00 23.50 C +ATOM 353 O PHE B 24 -17.092 4.530 -0.402 1.00 24.02 O +ATOM 354 CB PHE B 24 -15.811 2.837 -3.086 1.00 17.36 C +ATOM 355 CG PHE B 24 -16.428 1.661 -2.361 1.00 19.89 C +ATOM 356 CD1 PHE B 24 -15.628 0.691 -1.776 1.00 18.48 C +ATOM 357 CD2 PHE B 24 -17.811 1.527 -2.269 1.00 22.89 C +ATOM 358 CE1 PHE B 24 -16.189 -0.390 -1.107 1.00 21.90 C +ATOM 359 CE2 PHE B 24 -18.378 0.446 -1.597 1.00 19.48 C +ATOM 360 CZ PHE B 24 -17.562 -0.513 -1.015 1.00 19.73 C +ATOM 361 N PHE B 25 -17.742 5.048 -2.487 1.00 23.02 N +ATOM 362 CA PHE B 25 -19.108 5.343 -2.088 1.00 26.05 C +ATOM 363 C PHE B 25 -20.081 4.558 -2.948 1.00 29.87 C +ATOM 364 O PHE B 25 -19.912 4.448 -4.158 1.00 25.71 O +ATOM 365 CB PHE B 25 -19.410 6.848 -2.118 1.00 30.50 C +ATOM 366 CG PHE B 25 -19.035 7.523 -3.399 1.00 36.46 C +ATOM 367 CD1 PHE B 25 -17.729 7.929 -3.625 1.00 41.85 C +ATOM 368 CD2 PHE B 25 -19.989 7.772 -4.374 1.00 47.50 C +ATOM 369 CE1 PHE B 25 -17.376 8.562 -4.808 1.00 51.84 C +ATOM 370 CE2 PHE B 25 -19.645 8.407 -5.560 1.00 37.96 C +ATOM 371 CZ PHE B 25 -18.336 8.802 -5.778 1.00 47.77 C +ATOM 372 N TYR B 26 -21.090 3.991 -2.301 1.00 26.11 N +ATOM 373 CA TYR B 26 -22.087 3.184 -2.976 1.00 19.37 C +ATOM 374 C TYR B 26 -23.429 3.866 -2.826 1.00 26.37 C +ATOM 375 O TYR B 26 -23.966 3.954 -1.726 1.00 25.08 O +ATOM 376 CB TYR B 26 -22.136 1.795 -2.350 1.00 18.99 C +ATOM 377 CG TYR B 26 -23.255 0.930 -2.876 1.00 21.56 C +ATOM 378 CD1 TYR B 26 -24.280 0.506 -2.042 1.00 24.62 C +ATOM 379 CD2 TYR B 26 -23.285 0.533 -4.203 1.00 23.44 C +ATOM 380 CE1 TYR B 26 -25.304 -0.295 -2.516 1.00 26.30 C +ATOM 381 CE2 TYR B 26 -24.304 -0.265 -4.690 1.00 25.09 C +ATOM 382 CZ TYR B 26 -25.313 -0.675 -3.842 1.00 27.86 C +ATOM 383 OH TYR B 26 -26.328 -1.469 -4.320 1.00 29.25 O +ATOM 384 N THR B 27 -23.960 4.365 -3.936 1.00 28.14 N +ATOM 385 CA THR B 27 -25.185 5.147 -3.909 1.00 37.14 C +ATOM 386 C THR B 27 -26.169 4.594 -4.936 1.00 32.53 C +ATOM 387 O THR B 27 -26.193 5.035 -6.082 1.00 36.20 O +ATOM 388 CB THR B 27 -24.889 6.637 -4.188 1.00 36.89 C +ATOM 389 OG1 THR B 27 -24.271 6.772 -5.473 1.00 57.47 O +ATOM 390 CG2 THR B 27 -23.936 7.182 -3.151 1.00 33.01 C +ATOM 391 N PRO B 28 -26.989 3.620 -4.517 1.00 29.25 N +ATOM 392 CA PRO B 28 -27.893 2.887 -5.411 1.00 32.94 C +ATOM 393 C PRO B 28 -29.081 3.726 -5.872 1.00 32.76 C +ATOM 394 O PRO B 28 -29.671 3.417 -6.908 1.00 36.05 O +ATOM 395 CB PRO B 28 -28.401 1.730 -4.542 1.00 31.48 C +ATOM 396 CG PRO B 28 -27.658 1.813 -3.247 1.00 28.54 C +ATOM 397 CD PRO B 28 -27.128 3.190 -3.118 1.00 34.39 C +ATOM 398 N LYS B 29 -29.436 4.751 -5.105 1.00 34.79 N +ATOM 399 CA LYS B 29 -30.532 5.642 -5.483 1.00 49.07 C +ATOM 400 C LYS B 29 -30.051 6.834 -6.309 1.00 63.70 C +ATOM 401 O LYS B 29 -30.669 7.191 -7.315 1.00 73.47 O +ATOM 402 CB LYS B 29 -31.305 6.122 -4.251 1.00 62.86 C +ATOM 403 CG LYS B 29 -32.706 5.526 -4.105 1.00 74.15 C +ATOM 404 CD LYS B 29 -32.690 4.118 -3.525 1.00 72.32 C +ATOM 405 CE LYS B 29 -32.356 3.061 -4.572 1.00 68.55 C +ATOM 406 NZ LYS B 29 -33.458 2.854 -5.553 1.00 59.40 N +ATOM 407 N ALA B 30 -28.950 7.446 -5.884 1.00 72.05 N +ATOM 408 CA ALA B 30 -28.366 8.568 -6.616 1.00 74.07 C +ATOM 409 C ALA B 30 -27.782 8.115 -7.955 1.00 73.01 C +ATOM 410 O ALA B 30 -27.485 8.928 -8.831 1.00 64.47 O +ATOM 411 CB ALA B 30 -27.302 9.269 -5.772 1.00 56.14 C +ATOM 412 OXT ALA B 30 -27.594 6.921 -8.197 1.00 73.19 O +TER 413 ALA B 30 +HETATM 414 O HOH A 22 -29.500 -7.696 -14.149 1.00 50.68 O +HETATM 415 O HOH A 23 -11.374 10.214 -16.391 1.00 40.62 O +HETATM 416 O HOH A 24 -11.187 9.560 -19.007 1.00 44.09 O +HETATM 417 O HOH A 25 -22.708 -0.422 -18.245 1.00 25.03 O +HETATM 418 O HOH A 26 -17.282 8.923 0.122 1.00 44.14 O +HETATM 419 O HOH A 27 -27.802 -5.289 -20.151 1.00 41.02 O +HETATM 420 O HOH A 28 -13.732 9.674 -11.684 1.00 48.35 O +HETATM 421 O HOH A 29 -26.166 6.685 -14.912 1.00 50.84 O +HETATM 422 O HOH A 30 -30.826 -5.812 -17.868 1.00 54.11 O +HETATM 423 O HOH A 31 -14.803 9.989 -8.715 1.00 62.79 O +HETATM 424 O HOH A 32 -19.609 9.964 -9.626 1.00 46.30 O +HETATM 425 O HOH A 33 -13.690 11.749 -14.300 1.00 49.90 O +HETATM 426 O HOH B 31 -24.729 10.263 -12.014 1.00 61.01 O +HETATM 427 O HOH B 32 -20.724 -10.273 -19.319 1.00 52.72 O +HETATM 428 O HOH B 33 -17.700 -13.422 -2.674 1.00 25.54 O +HETATM 429 O HOH B 34 -28.494 10.301 -14.536 1.00 56.88 O +HETATM 430 O HOH B 35 -24.545 6.027 -8.162 1.00 32.84 O +HETATM 431 O HOH B 36 -27.182 -2.924 -7.024 1.00 27.65 O +HETATM 432 O HOH B 37 -24.782 -9.599 -9.935 1.00 26.60 O +HETATM 433 O HOH B 38 -14.505 -9.421 -15.869 1.00 44.83 O +HETATM 434 O HOH B 39 -28.442 -1.829 -2.831 1.00 43.18 O +HETATM 435 O HOH B 40 -12.046 -0.492 -0.930 1.00 25.29 O +HETATM 436 O HOH B 41 -18.702 -9.557 -7.601 1.00 29.84 O +HETATM 437 O HOH B 42 -8.200 -0.632 -9.134 1.00 32.65 O +HETATM 438 O HOH B 43 -15.277 -10.853 -7.465 1.00 43.14 O +HETATM 439 O HOH B 44 -22.107 4.402 -6.065 1.00 31.09 O +HETATM 440 O HOH B 45 -5.206 0.010 -2.235 1.00 43.01 O +HETATM 441 O HOH B 46 -26.729 -9.715 -6.146 1.00 30.80 O +HETATM 442 O HOH B 47 -27.875 3.972 -9.042 1.00 40.15 O +HETATM 443 O HOH B 48 -20.453 -7.642 -0.550 1.00 34.77 O +HETATM 444 O HOH B 49 -17.760 -10.041 -0.552 1.00 37.12 O +HETATM 445 O HOH B 50 -22.932 -10.505 -16.556 1.00 47.78 O +HETATM 446 O HOH B 51 -28.195 5.830 -2.571 1.00 53.39 O +HETATM 447 O HOH B 52 -17.118 -11.123 -18.586 1.00 52.94 O +HETATM 448 O HOH B 53 -27.581 8.994 -11.659 1.00 53.89 O +CONECT 43 76 +CONECT 49 231 +CONECT 76 43 +CONECT 162 321 +CONECT 231 49 +CONECT 321 162 +MASTER 279 0 0 4 0 0 0 6 438 2 6 5 +END diff --git a/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/cg.pdb b/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/cg.pdb new file mode 100644 index 000000000..62f92b3fa --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/cg.pdb @@ -0,0 +1,202 @@ +ATOM 1 BB GLY A 1 -26.214 5.188 -11.960 1.00 0.00 +ATOM 2 BB ILE A 2 -24.579 2.426 -10.878 1.00 0.00 +ATOM 3 SC1 ILE A 2 -22.689 2.117 -8.841 1.00 0.00 +ATOM 4 BB VAL A 3 -26.923 0.510 -11.441 1.00 0.00 +ATOM 5 SC1 VAL A 3 -28.478 0.258 -9.370 1.00 0.00 +ATOM 6 BB GLU A 4 -27.331 1.201 -14.450 1.00 0.00 +ATOM 7 SC1 GLU A 4 -29.596 3.447 -12.744 1.00 0.00 +ATOM 8 BB GLN A 5 -24.204 0.600 -15.231 1.00 0.00 +ATOM 9 SC1 GLN A 5 -24.318 3.659 -16.384 1.00 0.00 +ATOM 10 BB CYS A 6 -23.739 -2.413 -13.484 1.00 0.00 +ATOM 11 SC1 CYS A 6 -21.159 -0.853 -12.757 1.00 0.00 +ATOM 12 BB CYS A 7 -26.566 -3.952 -13.363 1.00 0.00 +ATOM 13 SC1 CYS A 7 -28.018 -4.248 -10.926 1.00 0.00 +ATOM 14 BB THR A 8 -28.416 -3.394 -15.895 1.00 0.00 +ATOM 15 SC1 THR A 8 -30.273 -1.747 -15.052 1.00 0.00 +ATOM 16 BB SER A 9 -25.502 -3.238 -16.879 1.00 0.00 +ATOM 17 SC1 SER A 9 -25.656 -1.139 -18.183 1.00 0.00 +ATOM 18 BB ILE A 10 -22.342 -3.480 -17.891 1.00 0.00 +ATOM 19 SC1 ILE A 10 -21.925 -6.128 -19.546 1.00 0.00 +ATOM 20 BB CYS A 11 -19.547 -3.283 -16.373 1.00 0.00 +ATOM 21 SC1 CYS A 11 -19.532 -2.461 -13.235 1.00 0.00 +ATOM 22 BB SER A 12 -16.557 -1.298 -15.386 1.00 0.00 +ATOM 23 SC1 SER A 12 -16.616 -0.075 -17.329 1.00 0.00 +ATOM 24 BB LEU A 13 -13.622 -0.165 -14.373 1.00 0.00 +ATOM 25 SC1 LEU A 13 -10.864 -1.358 -13.822 1.00 0.00 +ATOM 26 BB TYR A 14 -14.043 2.750 -15.061 1.00 0.00 +ATOM 27 SC1 TYR A 14 -13.689 3.649 -17.367 1.00 0.00 +ATOM 28 SC2 TYR A 14 -12.366 5.572 -18.171 1.00 0.00 +ATOM 29 SC3 TYR A 14 -14.543 5.959 -17.262 1.00 0.00 +ATOM 30 SC4 TYR A 14 -13.236 7.890 -18.061 1.00 0.00 +ATOM 31 BB GLN A 15 -16.690 3.121 -13.399 1.00 0.00 +ATOM 32 SC1 GLN A 15 -19.688 2.957 -16.205 1.00 0.00 +ATOM 33 BB LEU A 16 -15.872 2.123 -10.630 1.00 0.00 +ATOM 34 SC1 LEU A 16 -16.551 -1.202 -10.687 1.00 0.00 +ATOM 35 BB GLU A 17 -13.606 4.333 -10.175 1.00 0.00 +ATOM 36 SC1 GLU A 17 -10.014 2.704 -11.228 1.00 0.00 +ATOM 37 BB ASN A 18 -15.730 6.702 -9.928 1.00 0.00 +ATOM 38 SC1 ASN A 18 -16.058 7.347 -13.112 1.00 0.00 +ATOM 39 BB TYR A 19 -16.247 5.491 -6.728 1.00 0.00 +ATOM 40 SC1 TYR A 19 -18.506 4.783 -7.767 1.00 0.00 +ATOM 41 SC2 TYR A 19 -19.620 4.625 -9.953 1.00 0.00 +ATOM 42 SC3 TYR A 19 -20.574 6.024 -8.276 1.00 0.00 +ATOM 43 SC4 TYR A 19 -21.681 5.865 -10.478 1.00 0.00 +ATOM 44 BB CYS A 20 -13.741 6.276 -5.638 1.00 0.00 +ATOM 45 SC1 CYS A 20 -12.198 3.622 -6.609 1.00 0.00 +ATOM 46 BB ASN A 21 -11.590 8.161 -3.487 1.00 0.00 +ATOM 47 SC1 ASN A 21 -13.980 7.543 -0.874 1.00 0.00 +ATOM 48 BB PHE B 22 -14.889 -9.235 -12.595 1.00 0.00 +ATOM 49 SC1 PHE B 22 -13.433 -9.308 -10.515 1.00 0.00 +ATOM 50 SC2 PHE B 22 -12.977 -7.339 -9.231 1.00 0.00 +ATOM 51 SC3 PHE B 22 -11.466 -8.045 -9.996 1.00 0.00 +ATOM 52 BB VAL B 23 -16.057 -6.340 -13.945 1.00 0.00 +ATOM 53 SC1 VAL B 23 -14.069 -5.176 -12.987 1.00 0.00 +ATOM 54 BB ASN B 24 -17.316 -7.678 -16.779 1.00 0.00 +ATOM 55 SC1 ASN B 24 -14.700 -6.138 -17.874 1.00 0.00 +ATOM 56 BB GLN B 25 -20.482 -7.367 -15.543 1.00 0.00 +ATOM 57 SC1 GLN B 25 -19.481 -10.691 -13.750 1.00 0.00 +ATOM 58 BB HIS B 26 -23.181 -8.077 -13.813 1.00 0.00 +ATOM 59 SC1 HIS B 26 -25.237 -7.990 -15.537 1.00 0.00 +ATOM 60 SC2 HIS B 26 -25.588 -8.212 -17.924 1.00 0.00 +ATOM 61 SC3 HIS B 26 -26.347 -6.808 -17.197 1.00 0.00 +ATOM 62 BB LEU B 27 -23.652 -5.904 -10.860 1.00 0.00 +ATOM 63 SC1 LEU B 27 -20.344 -6.637 -10.929 1.00 0.00 +ATOM 64 BB CYS B 28 -25.384 -6.729 -7.834 1.00 0.00 +ATOM 65 SC1 CYS B 28 -27.467 -6.515 -10.303 1.00 0.00 +ATOM 66 BB GLY B 29 -25.239 -5.626 -4.921 1.00 0.00 +ATOM 67 BB SER B 30 -22.878 -7.441 -3.380 1.00 0.00 +ATOM 68 SC1 SER B 30 -23.803 -9.320 -2.306 1.00 0.00 +ATOM 69 BB HIS B 31 -21.310 -7.648 -6.061 1.00 0.00 +ATOM 70 SC1 HIS B 31 -22.776 -9.716 -7.085 1.00 0.00 +ATOM 71 SC2 HIS B 31 -23.657 -11.652 -5.914 1.00 0.00 +ATOM 72 SC3 HIS B 31 -23.687 -11.774 -7.662 1.00 0.00 +ATOM 73 BB LEU B 32 -20.752 -4.590 -6.348 1.00 0.00 +ATOM 74 SC1 LEU B 32 -22.399 -2.605 -8.009 1.00 0.00 +ATOM 75 BB VAL B 33 -19.438 -4.030 -3.597 1.00 0.00 +ATOM 76 SC1 VAL B 33 -21.172 -3.360 -1.827 1.00 0.00 +ATOM 77 BB GLU B 34 -17.129 -6.036 -4.003 1.00 0.00 +ATOM 78 SC1 GLU B 34 -17.435 -9.930 -4.064 1.00 0.00 +ATOM 79 BB ALA B 35 -15.860 -4.659 -6.467 1.00 0.00 +ATOM 80 SC1 ALA B 35 -17.065 -5.240 -8.157 1.00 0.00 +ATOM 81 BB LEU B 36 -15.321 -1.924 -5.174 1.00 0.00 +ATOM 82 SC1 LEU B 36 -18.053 -0.004 -5.861 1.00 0.00 +ATOM 83 BB TYR B 37 -13.465 -3.024 -2.980 1.00 0.00 +ATOM 84 SC1 TYR B 37 -14.257 -4.298 -1.073 1.00 0.00 +ATOM 85 SC2 TYR B 37 -12.751 -4.079 0.874 1.00 0.00 +ATOM 86 SC3 TYR B 37 -12.878 -6.177 -0.272 1.00 0.00 +ATOM 87 SC4 TYR B 37 -11.380 -5.985 1.667 1.00 0.00 +ATOM 88 BB LEU B 38 -11.290 -4.298 -4.867 1.00 0.00 +ATOM 89 SC1 LEU B 38 -12.200 -7.544 -4.847 1.00 0.00 +ATOM 90 BB VAL B 39 -10.668 -1.763 -6.631 1.00 0.00 +ATOM 91 SC1 VAL B 39 -12.123 -1.797 -8.776 1.00 0.00 +ATOM 92 BB CYS B 40 -10.236 0.613 -4.293 1.00 0.00 +ATOM 93 SC1 CYS B 40 -12.923 1.802 -5.236 1.00 0.00 +ATOM 94 BB GLY B 41 -9.225 -0.167 -1.672 1.00 0.00 +ATOM 95 BB GLU B 42 -7.795 2.278 0.434 1.00 0.00 +ATOM 96 SC1 GLU B 42 -4.051 2.070 1.072 1.00 0.00 +ATOM 97 BB ARG B 43 -9.760 4.457 -0.715 1.00 0.00 +ATOM 98 SC1 ARG B 43 -8.359 5.072 -3.683 1.00 0.00 +ATOM 99 SC2 ARG B 43 -8.247 3.708 -6.833 1.00 0.00 +ATOM 100 BB GLY B 44 -12.392 3.528 -1.251 1.00 0.00 +ATOM 101 BB PHE B 45 -16.063 4.216 -1.257 1.00 0.00 +ATOM 102 SC1 PHE B 45 -16.270 1.964 -2.548 1.00 0.00 +ATOM 103 SC2 PHE B 45 -16.333 -0.086 -1.292 1.00 0.00 +ATOM 104 SC3 PHE B 45 -18.015 0.557 -1.669 1.00 0.00 +ATOM 105 BB PHE B 46 -19.208 4.827 -2.996 1.00 0.00 +ATOM 106 SC1 PHE B 46 -19.132 7.352 -3.069 1.00 0.00 +ATOM 107 SC2 PHE B 46 -17.706 8.423 -4.668 1.00 0.00 +ATOM 108 SC3 PHE B 46 -19.449 8.303 -5.245 1.00 0.00 +ATOM 109 BB TYR B 47 -22.683 3.773 -2.397 1.00 0.00 +ATOM 110 SC1 TYR B 47 -22.696 1.363 -2.613 1.00 0.00 +ATOM 111 SC2 TYR B 47 -24.792 0.105 -2.279 1.00 0.00 +ATOM 112 SC3 TYR B 47 -23.794 0.134 -4.447 1.00 0.00 +ATOM 113 SC4 TYR B 47 -25.893 -1.129 -4.115 1.00 0.00 +ATOM 114 BB THR B 48 -25.385 4.788 -4.788 1.00 0.00 +ATOM 115 SC1 THR B 48 -24.356 6.854 -4.391 1.00 0.00 +ATOM 116 BB PRO B 49 -28.449 3.421 -5.725 1.00 0.00 +ATOM 117 SC1 PRO B 49 -27.729 2.244 -3.636 1.00 0.00 +ATOM 118 BB LYS B 50 -30.182 6.135 -6.111 1.00 0.00 +ATOM 119 SC1 LYS B 50 -32.234 5.255 -3.960 1.00 0.00 +ATOM 120 SC2 LYS B 50 -32.949 2.950 -5.100 1.00 0.00 +ATOM 121 BB ALA B 51 -28.005 7.972 -7.567 1.00 0.00 +ATOM 122 SC1 ALA B 51 -27.302 9.269 -5.772 1.00 0.00 +TER 123 ALA B 51 +CONECT 1 2 +CONECT 2 3 4 +CONECT 4 5 6 +CONECT 6 7 8 +CONECT 8 9 10 +CONECT 10 11 12 +CONECT 11 21 +CONECT 12 13 14 +CONECT 13 16 65 +CONECT 14 15 16 +CONECT 16 17 18 +CONECT 18 19 20 +CONECT 20 21 22 +CONECT 22 23 24 +CONECT 24 25 26 +CONECT 26 27 31 +CONECT 27 28 29 +CONECT 28 29 30 +CONECT 29 30 +CONECT 31 32 33 +CONECT 33 34 35 +CONECT 35 36 37 +CONECT 37 38 39 +CONECT 39 40 44 +CONECT 40 41 42 +CONECT 41 42 43 +CONECT 42 43 +CONECT 44 45 46 +CONECT 45 93 +CONECT 46 47 +CONECT 48 49 52 +CONECT 49 50 51 +CONECT 50 51 +CONECT 52 53 54 +CONECT 54 55 56 +CONECT 56 57 58 +CONECT 58 59 62 +CONECT 59 60 61 +CONECT 60 61 +CONECT 62 63 64 +CONECT 64 65 66 +CONECT 66 67 +CONECT 67 68 69 +CONECT 69 70 73 +CONECT 70 71 72 +CONECT 71 72 +CONECT 73 74 75 +CONECT 75 76 77 +CONECT 77 78 79 +CONECT 79 80 81 +CONECT 81 82 83 +CONECT 83 84 88 +CONECT 84 85 86 +CONECT 85 86 87 +CONECT 86 87 +CONECT 88 89 90 +CONECT 90 91 92 +CONECT 92 93 94 +CONECT 94 95 +CONECT 95 96 97 +CONECT 97 98 100 +CONECT 98 99 +CONECT 100 101 +CONECT 101 102 105 +CONECT 102 103 104 +CONECT 103 104 +CONECT 105 106 109 +CONECT 106 107 108 +CONECT 107 108 +CONECT 109 110 114 +CONECT 110 111 112 +CONECT 111 112 113 +CONECT 112 113 +CONECT 114 115 116 +CONECT 116 117 118 +CONECT 118 119 121 +CONECT 119 120 +CONECT 121 122 +END \ No newline at end of file diff --git a/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/cg.top b/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/cg.top new file mode 100644 index 000000000..a45ed27af --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/cg.top @@ -0,0 +1,9 @@ + +#include "martini.itp" +#include "molecule_0.itp" + +[ system ] +Title of the system + +[ molecules ] +molecule_0 1 diff --git a/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/citation b/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/citation new file mode 100644 index 000000000..ddb39213d --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/citation @@ -0,0 +1 @@ +Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 diff --git a/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/command new file mode 100644 index 000000000..c90fbbed5 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/command @@ -0,0 +1,12 @@ +martinize2 +-f ../aa.pdb +-o cg.top +-x cg.pdb +-dssp +-p backbone +-ff martini3001 +-scfix +-cys auto +-ignore HOH +-elastic +-ew diff --git a/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/en_bonds.itp b/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/en_bonds.itp new file mode 100644 index 000000000..f898478df --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/en_bonds.itp @@ -0,0 +1,189 @@ +[ bonds ] +1 6 1 0.4832 500.0 +1 8 1 0.59829 500.0 +1 10 1 0.81378 500.0 +1 114 1 0.72304 500.0 +1 116 1 0.68548 500.0 +1 118 1 0.713 500.0 +1 121 1 0.55001 500.0 +2 8 1 0.47356 500.0 +2 10 1 0.55601 500.0 +2 12 1 0.71275 500.0 +2 14 1 0.85886 500.0 +2 16 1 0.8304 500.0 +2 31 1 0.83117 500.0 +2 33 1 0.87161 500.0 +2 62 1 0.8382 500.0 +2 109 1 0.87932 500.0 +2 114 1 0.6581 500.0 +2 116 1 0.65204 500.0 +2 118 1 0.82376 500.0 +2 121 1 0.73109 500.0 +4 10 1 0.47804 500.0 +4 12 1 0.4871 500.0 +4 14 1 0.61074 500.0 +4 16 1 0.67557 500.0 +4 18 1 0.88603 500.0 +4 62 1 0.72237 500.0 +4 64 1 0.82327 500.0 +4 114 1 0.8058 500.0 +4 116 1 0.65933 500.0 +4 118 1 0.84061 500.0 +4 121 1 0.84769 500.0 +6 12 1 0.53207 500.0 +6 14 1 0.49367 500.0 +6 16 1 0.53802 500.0 +6 18 1 0.76576 500.0 +6 62 1 0.87694 500.0 +8 14 1 0.58417 500.0 +8 16 1 0.43738 500.0 +8 18 1 0.5214 500.0 +8 22 1 0.78801 500.0 +8 31 1 0.8135 500.0 +8 56 1 0.87987 500.0 +8 58 1 0.88507 500.0 +8 62 1 0.78556 500.0 +10 31 1 0.89626 500.0 +10 52 1 0.86403 500.0 +10 54 1 0.89356 500.0 +10 56 1 0.62764 500.0 +10 58 1 0.57009 500.0 +10 62 1 0.43686 500.0 +10 73 1 0.80365 500.0 +12 56 1 0.73099 500.0 +12 58 1 0.53553 500.0 +14 20 1 0.88825 500.0 +14 56 1 0.88806 500.0 +14 58 1 0.73262 500.0 +14 62 1 0.73725 500.0 +16 56 1 0.66365 500.0 +16 58 1 0.61811 500.0 +16 62 1 0.6839 500.0 +18 52 1 0.79528 500.0 +18 54 1 0.66421 500.0 +18 56 1 0.49073 500.0 +18 58 1 0.62018 500.0 +18 62 1 0.75519 500.0 +20 26 1 0.82714 500.0 +20 31 1 0.76172 500.0 +20 33 1 0.87015 500.0 +20 48 1 0.84494 500.0 +20 52 1 0.52365 500.0 +20 54 1 0.49452 500.0 +20 56 1 0.42704 500.0 +20 58 1 0.65369 500.0 +20 62 1 0.73562 500.0 +22 31 1 0.48467 500.0 +22 33 1 0.58986 500.0 +22 35 1 0.82201 500.0 +22 48 1 0.85778 500.0 +22 52 1 0.52685 500.0 +22 54 1 0.65741 500.0 +22 56 1 0.72288 500.0 +24 33 1 0.49302 500.0 +24 35 1 0.61525 500.0 +24 37 1 0.84473 500.0 +24 52 1 0.66519 500.0 +24 54 1 0.87104 500.0 +24 90 1 0.84391 500.0 +26 35 1 0.51543 500.0 +26 37 1 0.6694 500.0 +31 37 1 0.50787 500.0 +31 39 1 0.70937 500.0 +31 44 1 0.88821 500.0 +33 39 1 0.51681 500.0 +33 44 1 0.68346 500.0 +33 79 1 0.79586 500.0 +33 81 1 0.68158 500.0 +33 90 1 0.76272 500.0 +33 92 1 0.86143 500.0 +33 105 1 0.87594 500.0 +35 44 1 0.49379 500.0 +35 46 1 0.79656 500.0 +35 81 1 0.81914 500.0 +35 90 1 0.76386 500.0 +35 92 1 0.77327 500.0 +37 46 1 0.77947 500.0 +37 105 1 0.79794 500.0 +39 81 1 0.76321 500.0 +39 97 1 0.8905 500.0 +39 100 1 0.6979 500.0 +39 101 1 0.56199 500.0 +39 105 1 0.481 500.0 +39 109 1 0.79454 500.0 +44 81 1 0.83636 500.0 +44 97 1 0.65868 500.0 +44 100 1 0.5349 500.0 +44 101 1 0.53687 500.0 +44 105 1 0.62426 500.0 +46 94 1 0.88457 500.0 +46 95 1 0.80238 500.0 +46 97 1 0.49744 500.0 +46 100 1 0.52059 500.0 +46 101 1 0.63675 500.0 +46 105 1 0.83307 500.0 +48 56 1 0.65919 500.0 +48 58 1 0.84603 500.0 +48 79 1 0.771 500.0 +52 58 1 0.73333 500.0 +52 62 1 0.8209 500.0 +52 79 1 0.76673 500.0 +54 62 1 0.88509 500.0 +58 69 1 0.79857 500.0 +58 73 1 0.85897 500.0 +62 67 1 0.76747 500.0 +62 69 1 0.56165 500.0 +62 73 1 0.55218 500.0 +62 75 1 0.86036 500.0 +64 69 1 0.45366 500.0 +64 73 1 0.53138 500.0 +64 75 1 0.77842 500.0 +66 73 1 0.4821 500.0 +66 75 1 0.61604 500.0 +66 77 1 0.81712 500.0 +67 75 1 0.48496 500.0 +67 77 1 0.59509 500.0 +67 79 1 0.81562 500.0 +69 77 1 0.49312 500.0 +69 79 1 0.62294 500.0 +69 81 1 0.83323 500.0 +73 79 1 0.48939 500.0 +73 81 1 0.61629 500.0 +73 83 1 0.81794 500.0 +75 81 1 0.48859 500.0 +75 83 1 0.60888 500.0 +75 88 1 0.82503 500.0 +75 105 1 0.88798 500.0 +75 109 1 0.85352 500.0 +77 83 1 0.48527 500.0 +77 88 1 0.6153 500.0 +77 90 1 0.81796 500.0 +79 88 1 0.48547 500.0 +79 90 1 0.59471 500.0 +79 92 1 0.80095 500.0 +81 90 1 0.48783 500.0 +81 92 1 0.57507 500.0 +81 94 1 0.72464 500.0 +81 100 1 0.73275 500.0 +81 101 1 0.73204 500.0 +81 105 1 0.80887 500.0 +83 92 1 0.50376 500.0 +83 94 1 0.52769 500.0 +83 95 1 0.84802 500.0 +83 97 1 0.86499 500.0 +83 100 1 0.6861 500.0 +83 101 1 0.78829 500.0 +88 94 1 0.56152 500.0 +88 100 1 0.86908 500.0 +90 95 1 0.86316 500.0 +90 97 1 0.86323 500.0 +90 100 1 0.77404 500.0 +92 97 1 0.52729 500.0 +92 100 1 0.47326 500.0 +92 101 1 0.74935 500.0 +94 100 1 0.48855 500.0 +94 101 1 0.81335 500.0 +95 101 1 0.86594 500.0 +109 118 1 0.86945 500.0 +109 121 1 0.85247 500.0 +114 121 1 0.49721 500.0 diff --git a/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/molecule_0.itp b/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/molecule_0.itp new file mode 100644 index 000000000..d9f84331d --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/EN_ext/martinize2/molecule_0.itp @@ -0,0 +1,718 @@ +; This file was generated using the following command: +; /coarse/chris/python_packages/vermouth_dev/vermouth-martinize/venv/bin/martinize2 -f aa.pdb -o cg.top -x cg.pdb -dssp -p backbone -ff martini3001 -scfix -cys auto -ignore HOH -elastic -ew +; martinize with vermouth 0.0.1.dev1767 +; The following sequence of secondary structure +; was used for the full system: +; CHIIIIITTTCCHHHHHTTBCCCSSCCCTHHHHHHHHHHHGGGCBCCCSCC + +; Please cite the following papers: +; McGibbon, R T; Beauchamp, K A; Harrigan, M P; Klein, C; Swails, J M; Hernández, C X; Schwantes, C R; Wang, L; Lane, T J; Pande, V S; Biophysical Journal 2015; 10.1016/j.bpj.2015.08.015 +; Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 + +[ moleculetype ] +molecule_0 1 + +[ atoms ] + 1 Q5 1 GLY BB 1 1 + 2 P2 2 ILE BB 2 0.0 + 3 SC2 2 ILE SC1 3 0.0 + 4 SP2 3 VAL BB 4 0.0 + 5 SC3 3 VAL SC1 5 0.0 + 6 P2 4 GLU BB 6 0.0 + 7 Q5n 4 GLU SC1 7 -1.0 + 8 P2 5 GLN BB 8 0.0 + 9 P5 5 GLN SC1 9 0.0 + 10 P2 6 CYS BB 10 0.0 + 11 TC6 6 CYS SC1 11 0.0 + 12 P2 7 CYS BB 12 0.0 + 13 TC6 7 CYS SC1 13 0.0 + 14 P2 8 THR BB 14 0.0 + 15 SP1 8 THR SC1 15 0.0 + 16 P2 9 SER BB 16 0.0 + 17 TP1 9 SER SC1 17 0.0 + 18 P2 10 ILE BB 18 0.0 + 19 SC2 10 ILE SC1 19 0.0 + 20 P2 11 CYS BB 20 0.0 + 21 TC6 11 CYS SC1 21 0.0 + 22 P2 12 SER BB 22 0.0 + 23 TP1 12 SER SC1 23 0.0 + 24 P2 13 LEU BB 24 0.0 + 25 SC2 13 LEU SC1 25 0.0 + 26 P2 14 TYR BB 26 0.0 + 27 TC4 14 TYR SC1 27 0.0 + 28 TC5 14 TYR SC2 28 0.0 + 29 TC5 14 TYR SC3 29 0.0 + 30 TN6 14 TYR SC4 30 0.0 + 31 P2 15 GLN BB 31 0.0 + 32 P5 15 GLN SC1 32 0.0 + 33 P2 16 LEU BB 33 0.0 + 34 SC2 16 LEU SC1 34 0.0 + 35 P2 17 GLU BB 35 0.0 + 36 Q5n 17 GLU SC1 36 -1.0 + 37 P2 18 ASN BB 37 0.0 + 38 SP5 18 ASN SC1 38 0.0 + 39 P2 19 TYR BB 39 0.0 + 40 TC4 19 TYR SC1 40 0.0 + 41 TC5 19 TYR SC2 41 0.0 + 42 TC5 19 TYR SC3 42 0.0 + 43 TN6 19 TYR SC4 43 0.0 + 44 P2 20 CYS BB 44 0.0 + 45 TC6 20 CYS SC1 45 0.0 + 46 Q5 21 ASN BB 46 -1 + 47 SP5 21 ASN SC1 47 0.0 + 48 Q5 22 PHE BB 48 1 + 49 SC4 22 PHE SC1 49 0.0 + 50 TC5 22 PHE SC2 50 0.0 + 51 TC5 22 PHE SC3 51 0.0 + 52 SP2 23 VAL BB 52 0.0 + 53 SC3 23 VAL SC1 53 0.0 + 54 P2 24 ASN BB 54 0.0 + 55 SP5 24 ASN SC1 55 0.0 + 56 P2 25 GLN BB 56 0.0 + 57 P5 25 GLN SC1 57 0.0 + 58 P2 26 HIS BB 58 0.0 + 59 TC4 26 HIS SC1 59 0.0 + 60 TN6d 26 HIS SC2 60 0.0 + 61 TN5a 26 HIS SC3 61 0.0 + 62 P2 27 LEU BB 62 0.0 + 63 SC2 27 LEU SC1 63 0.0 + 64 P2 28 CYS BB 64 0.0 + 65 TC6 28 CYS SC1 65 0.0 + 66 SP1 29 GLY BB 66 0.0 + 67 P2 30 SER BB 67 0.0 + 68 TP1 30 SER SC1 68 0.0 + 69 P2 31 HIS BB 69 0.0 + 70 TC4 31 HIS SC1 70 0.0 + 71 TN6d 31 HIS SC2 71 0.0 + 72 TN5a 31 HIS SC3 72 0.0 + 73 P2 32 LEU BB 73 0.0 + 74 SC2 32 LEU SC1 74 0.0 + 75 SP2 33 VAL BB 75 0.0 + 76 SC3 33 VAL SC1 76 0.0 + 77 P2 34 GLU BB 77 0.0 + 78 Q5n 34 GLU SC1 78 -1.0 + 79 SP2 35 ALA BB 79 0.0 + 80 TC3 35 ALA SC1 80 0.0 + 81 P2 36 LEU BB 81 0.0 + 82 SC2 36 LEU SC1 82 0.0 + 83 P2 37 TYR BB 83 0.0 + 84 TC4 37 TYR SC1 84 0.0 + 85 TC5 37 TYR SC2 85 0.0 + 86 TC5 37 TYR SC3 86 0.0 + 87 TN6 37 TYR SC4 87 0.0 + 88 P2 38 LEU BB 88 0.0 + 89 SC2 38 LEU SC1 89 0.0 + 90 SP2 39 VAL BB 90 0.0 + 91 SC3 39 VAL SC1 91 0.0 + 92 P2 40 CYS BB 92 0.0 + 93 TC6 40 CYS SC1 93 0.0 + 94 SP1 41 GLY BB 94 0.0 + 95 P2 42 GLU BB 95 0.0 + 96 Q5n 42 GLU SC1 96 -1.0 + 97 P2 43 ARG BB 97 0.0 + 98 SC3 43 ARG SC1 98 0.0 + 99 SQ3p 43 ARG SC2 99 1.0 +100 SP1 44 GLY BB 100 0.0 +101 P2 45 PHE BB 101 0.0 +102 SC4 45 PHE SC1 102 0.0 +103 TC5 45 PHE SC2 103 0.0 +104 TC5 45 PHE SC3 104 0.0 +105 P2 46 PHE BB 105 0.0 +106 SC4 46 PHE SC1 106 0.0 +107 TC5 46 PHE SC2 107 0.0 +108 TC5 46 PHE SC3 108 0.0 +109 P2 47 TYR BB 109 0.0 +110 TC4 47 TYR SC1 110 0.0 +111 TC5 47 TYR SC2 111 0.0 +112 TC5 47 TYR SC3 112 0.0 +113 TN6 47 TYR SC4 113 0.0 +114 P2 48 THR BB 114 0.0 +115 SP1 48 THR SC1 115 0.0 +116 SP2a 49 PRO BB 116 0.0 +117 SC3 49 PRO SC1 117 0.0 +118 P2 50 LYS BB 118 0.0 +119 SC3 50 LYS SC1 119 0.0 +120 SQ4p 50 LYS SC2 120 1.0 +121 Q5 51 ALA BB 121 -1 +122 TC3 51 ALA SC1 122 0.0 + +[ position_restraints ] +#ifdef POSRES + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 4 1 1000 1000 1000 + 6 1 1000 1000 1000 + 8 1 1000 1000 1000 + 10 1 1000 1000 1000 + 12 1 1000 1000 1000 + 14 1 1000 1000 1000 + 16 1 1000 1000 1000 + 18 1 1000 1000 1000 + 20 1 1000 1000 1000 + 22 1 1000 1000 1000 + 24 1 1000 1000 1000 + 26 1 1000 1000 1000 + 31 1 1000 1000 1000 + 33 1 1000 1000 1000 + 35 1 1000 1000 1000 + 37 1 1000 1000 1000 + 39 1 1000 1000 1000 + 44 1 1000 1000 1000 + 46 1 1000 1000 1000 + 48 1 1000 1000 1000 + 52 1 1000 1000 1000 + 54 1 1000 1000 1000 + 56 1 1000 1000 1000 + 58 1 1000 1000 1000 + 62 1 1000 1000 1000 + 64 1 1000 1000 1000 + 66 1 1000 1000 1000 + 67 1 1000 1000 1000 + 69 1 1000 1000 1000 + 73 1 1000 1000 1000 + 75 1 1000 1000 1000 + 77 1 1000 1000 1000 + 79 1 1000 1000 1000 + 81 1 1000 1000 1000 + 83 1 1000 1000 1000 + 88 1 1000 1000 1000 + 90 1 1000 1000 1000 + 92 1 1000 1000 1000 + 94 1 1000 1000 1000 + 95 1 1000 1000 1000 + 97 1 1000 1000 1000 +100 1 1000 1000 1000 +101 1 1000 1000 1000 +105 1 1000 1000 1000 +109 1 1000 1000 1000 +114 1 1000 1000 1000 +116 1 1000 1000 1000 +118 1 1000 1000 1000 +121 1 1000 1000 1000 +#endif + +[ bonds ] +; Backbone bonds + 14 16 1 0.350 4000 + 16 18 1 0.350 4000 + 18 20 1 0.350 4000 + 20 22 1 0.350 4000 + 37 39 1 0.350 4000 + 39 44 1 0.350 4000 + 44 46 1 0.350 4000 + 48 52 1 0.350 4000 + 52 54 1 0.350 4000 + 54 56 1 0.350 4000 + 56 58 1 0.350 4000 + 58 62 1 0.350 4000 + 62 64 1 0.350 4000 + 64 66 1 0.350 4000 +100 101 1 0.350 4000 +101 105 1 0.350 4000 +105 109 1 0.350 4000 +109 114 1 0.350 4000 +114 116 1 0.350 4000 +116 118 1 0.350 4000 +118 121 1 0.350 4000 + +; Side chain bonds + 6 7 1 0.400 5000 + 8 9 1 0.400 5000 + 10 11 1 0.341 7500 + 12 13 1 0.341 7500 + 16 17 1 0.287 7500 + 20 21 1 0.341 7500 + 22 23 1 0.287 7500 + 24 25 1 0.363 7500 + 26 27 1 0.325 5000 + 31 32 1 0.400 5000 + 33 34 1 0.363 7500 + 35 36 1 0.400 5000 + 37 38 1 0.352 5000 + 39 40 1 0.325 5000 + 44 45 1 0.341 7500 + 46 47 1 0.352 5000 + 48 49 1 0.325 7500 + 54 55 1 0.352 5000 + 56 57 1 0.400 5000 + 58 59 1 0.336 7500 + 62 63 1 0.363 7500 + 64 65 1 0.341 7500 + 67 68 1 0.287 7500 + 69 70 1 0.336 7500 + 73 74 1 0.363 7500 + 77 78 1 0.400 5000 + 81 82 1 0.363 7500 + 83 84 1 0.325 5000 + 88 89 1 0.363 7500 + 92 93 1 0.341 7500 + 95 96 1 0.400 5000 + 97 98 1 0.330 5000 + 98 99 1 0.380 5000 +101 102 1 0.325 7500 +105 106 1 0.325 7500 +109 110 1 0.325 5000 +116 117 1 0.330 7500 +118 119 1 0.330 5000 +119 120 1 0.360 5000 + +#ifdef FLEXIBLE +; Side chain bonds + 2 3 1 0.341 1000000 + 4 5 1 0.292 1000000 + 14 15 1 0.305 1000000 + 18 19 1 0.341 1000000 + 27 28 1 0.300 1000000 + 27 29 1 0.300 1000000 + 28 30 1 0.285 1000000 + 29 30 1 0.285 1000000 + 28 29 1 0.300 1000000 + 40 41 1 0.300 1000000 + 40 42 1 0.300 1000000 + 41 43 1 0.285 1000000 + 42 43 1 0.285 1000000 + 41 42 1 0.300 1000000 + 49 50 1 0.340 1000000 + 49 51 1 0.340 1000000 + 50 51 1 0.290 1000000 + 52 53 1 0.292 1000000 + 59 60 1 0.320 1000000 + 59 61 1 0.300 1000000 + 60 61 1 0.270 1000000 + 70 71 1 0.320 1000000 + 70 72 1 0.300 1000000 + 71 72 1 0.270 1000000 + 75 76 1 0.292 1000000 + 79 80 1 0.270 1000000 + 84 85 1 0.300 1000000 + 84 86 1 0.300 1000000 + 85 87 1 0.285 1000000 + 86 87 1 0.285 1000000 + 85 86 1 0.300 1000000 + 90 91 1 0.292 1000000 +102 103 1 0.340 1000000 +102 104 1 0.340 1000000 +103 104 1 0.290 1000000 +106 107 1 0.340 1000000 +106 108 1 0.340 1000000 +107 108 1 0.290 1000000 +110 111 1 0.300 1000000 +110 112 1 0.300 1000000 +111 113 1 0.285 1000000 +112 113 1 0.285 1000000 +111 112 1 0.300 1000000 +114 115 1 0.305 1000000 +121 122 1 0.270 1000000 +#endif + +[ constraints ] + 11 21 1 0.24 ; Disulfide bridge + 13 65 1 0.24 ; Disulfide bridge + 45 93 1 0.24 ; Disulfide bridge + +; Backbone bonds + 1 2 1 0.33 + 2 4 1 0.310 + 4 6 1 0.310 + 6 8 1 0.310 + 8 10 1 0.310 + 10 12 1 0.310 + 12 14 1 0.33 + 22 24 1 0.33 + 24 26 1 0.310 + 26 31 1 0.310 + 31 33 1 0.310 + 33 35 1 0.310 + 35 37 1 0.33 + 66 67 1 0.33 + 67 69 1 0.310 + 69 73 1 0.310 + 73 75 1 0.310 + 75 77 1 0.310 + 77 79 1 0.310 + 79 81 1 0.310 + 81 83 1 0.310 + 83 88 1 0.310 + 88 90 1 0.310 + 90 92 1 0.310 + 92 94 1 0.310 + 94 95 1 0.310 + 95 97 1 0.310 + 97 100 1 0.33 + +#ifndef FLEXIBLE +; Side chain bonds + 2 3 1 0.341 + 4 5 1 0.292 + 14 15 1 0.305 + 18 19 1 0.341 + 27 28 1 0.300 + 27 29 1 0.300 + 28 30 1 0.285 + 29 30 1 0.285 + 28 29 1 0.300 + 40 41 1 0.300 + 40 42 1 0.300 + 41 43 1 0.285 + 42 43 1 0.285 + 41 42 1 0.300 + 49 50 1 0.340 + 49 51 1 0.340 + 50 51 1 0.290 + 52 53 1 0.292 + 59 60 1 0.320 + 59 61 1 0.300 + 60 61 1 0.270 + 70 71 1 0.320 + 70 72 1 0.300 + 71 72 1 0.270 + 75 76 1 0.292 + 79 80 1 0.270 + 84 85 1 0.300 + 84 86 1 0.300 + 85 87 1 0.285 + 86 87 1 0.285 + 85 86 1 0.300 + 90 91 1 0.292 +102 103 1 0.340 +102 104 1 0.340 +103 104 1 0.290 +106 107 1 0.340 +106 108 1 0.340 +107 108 1 0.290 +110 111 1 0.300 +110 112 1 0.300 +111 113 1 0.285 +112 113 1 0.285 +111 112 1 0.300 +114 115 1 0.305 +121 122 1 0.270 +#endif + +#ifdef ELASTIC +#include "en_bonds.itp" +#endif + +[ angles ] +; BBB angles + 1 2 4 10 127 20 + 2 4 6 2 96 700 + 4 6 8 2 96 700 + 6 8 10 2 96 700 + 8 10 12 2 96 700 + 10 12 14 10 100 20 + 12 14 16 10 100 20 + 20 22 24 10 127 20 + 22 24 26 10 127 20 + 24 26 31 2 96 700 + 26 31 33 2 96 700 + 31 33 35 2 96 700 + 33 35 37 10 100 20 + 35 37 39 10 100 20 + 64 66 67 10 100 20 + 66 67 69 10 100 20 + 67 69 73 2 96 700 + 69 73 75 2 96 700 + 73 75 77 2 96 700 + 75 77 79 2 96 700 + 77 79 81 2 96 700 + 79 81 83 2 96 700 + 81 83 88 2 96 700 + 83 88 90 2 96 700 + 88 90 92 2 96 700 + 90 92 94 2 96 700 + 92 94 95 2 96 700 + 94 95 97 2 96 700 + 95 97 100 10 127 20 + 97 100 101 10 127 20 + 37 39 44 10 100 20 + 39 44 46 10 100 20 +100 101 105 10 127 20 +101 105 109 10 127 20 +109 114 116 10 127 20 +114 116 118 10 127 20 +116 118 121 10 127 20 + 48 52 54 10 127 20 + 52 54 56 10 127 20 + 54 56 58 10 127 20 + 56 58 62 10 127 20 + 16 18 20 10 100 20 + 18 20 22 10 100 20 + 58 62 64 10 127 20 + 62 64 66 10 100 20 +105 109 114 10 127 20 + 14 16 18 10 100 20 + +; BBS angles regular martini + 1 2 3 2 100 25 + 2 4 5 2 100 25 + 4 6 7 2 100 25 + 6 8 9 2 100 25 + 8 10 11 2 100 25 + 10 12 13 2 100 25 + 12 14 15 2 100 25 + 14 16 17 2 100 25 + 16 18 19 2 100 25 + 18 20 21 2 100 25 + 20 22 23 2 100 25 + 22 24 25 2 100 25 + 24 26 27 2 100 25 + 26 31 32 2 100 25 + 31 33 34 2 100 25 + 33 35 36 2 100 25 + 35 37 38 2 100 25 + 37 39 40 2 100 25 + 39 44 45 2 100 25 + 44 46 47 2 100 25 + 48 52 53 2 100 25 + 52 54 55 2 100 25 + 54 56 57 2 100 25 + 56 58 59 2 100 25 + 58 62 63 2 100 25 + 62 64 65 2 100 25 + 66 67 68 2 100 25 + 67 69 70 2 100 25 + 69 73 74 2 100 25 + 73 75 76 2 100 25 + 75 77 78 2 100 25 + 77 79 80 2 100 25 + 79 81 82 2 100 25 + 81 83 84 2 100 25 + 83 88 89 2 100 25 + 88 90 91 2 100 25 + 90 92 93 2 100 25 + 94 95 96 2 100 25 + 95 97 98 2 100 25 +100 101 102 2 100 25 +101 105 106 2 100 25 +105 109 110 2 100 25 +109 114 115 2 100 25 +114 116 117 2 100 25 +116 118 119 2 100 25 +118 121 122 2 100 25 + +; First SBB regular martini + 49 48 52 2 100 25 + +; SC-BB-BB and BB-BB-SC scFix + 3 2 4 10 100 15 ; SC-BB-BB + 5 4 6 10 100 15 ; SC-BB-BB + 7 6 8 10 100 15 ; SC-BB-BB + 9 8 10 10 100 15 ; SC-BB-BB + 11 10 12 10 100 15 ; SC-BB-BB + 13 12 14 10 100 15 ; SC-BB-BB + 15 14 16 10 100 15 ; SC-BB-BB + 17 16 18 10 100 15 ; SC-BB-BB + 19 18 20 10 100 15 ; SC-BB-BB + 21 20 22 10 100 15 ; SC-BB-BB + 23 22 24 10 100 15 ; SC-BB-BB + 25 24 26 10 100 15 ; SC-BB-BB + 27 26 31 10 100 15 ; SC-BB-BB + 32 31 33 10 100 15 ; SC-BB-BB + 34 33 35 10 100 15 ; SC-BB-BB + 36 35 37 10 100 15 ; SC-BB-BB + 38 37 39 10 100 15 ; SC-BB-BB + 40 39 44 10 100 15 ; SC-BB-BB + 45 44 46 10 100 15 ; SC-BB-BB + 49 48 52 10 100 15 ; SC-BB-BB + 53 52 54 10 100 15 ; SC-BB-BB + 55 54 56 10 100 15 ; SC-BB-BB + 57 56 58 10 100 15 ; SC-BB-BB + 59 58 62 10 100 15 ; SC-BB-BB + 63 62 64 10 100 15 ; SC-BB-BB + 65 64 66 10 100 15 ; SC-BB-BB + 68 67 69 10 100 15 ; SC-BB-BB + 70 69 73 10 100 15 ; SC-BB-BB + 74 73 75 10 100 15 ; SC-BB-BB + 76 75 77 10 100 15 ; SC-BB-BB + 78 77 79 10 100 15 ; SC-BB-BB + 80 79 81 10 100 15 ; SC-BB-BB + 82 81 83 10 100 15 ; SC-BB-BB + 84 83 88 10 100 15 ; SC-BB-BB + 89 88 90 10 100 15 ; SC-BB-BB + 91 90 92 10 100 15 ; SC-BB-BB + 93 92 94 10 100 15 ; SC-BB-BB + 96 95 97 10 100 15 ; SC-BB-BB + 98 97 100 10 100 15 ; SC-BB-BB +102 101 105 10 100 15 ; SC-BB-BB +106 105 109 10 100 15 ; SC-BB-BB +110 109 114 10 100 15 ; SC-BB-BB +115 114 116 10 100 15 ; SC-BB-BB +117 116 118 10 100 15 ; SC-BB-BB +119 118 121 10 100 15 ; SC-BB-BB + 1 2 3 10 100 15 ; BB-BB-SC + 2 4 5 10 100 15 ; BB-BB-SC + 4 6 7 10 100 15 ; BB-BB-SC + 6 8 9 10 100 15 ; BB-BB-SC + 8 10 11 10 100 15 ; BB-BB-SC + 10 12 13 10 100 15 ; BB-BB-SC + 12 14 15 10 100 15 ; BB-BB-SC + 14 16 17 10 100 15 ; BB-BB-SC + 16 18 19 10 100 15 ; BB-BB-SC + 18 20 21 10 100 15 ; BB-BB-SC + 20 22 23 10 100 15 ; BB-BB-SC + 22 24 25 10 100 15 ; BB-BB-SC + 24 26 27 10 100 15 ; BB-BB-SC + 26 31 32 10 100 15 ; BB-BB-SC + 31 33 34 10 100 15 ; BB-BB-SC + 33 35 36 10 100 15 ; BB-BB-SC + 35 37 38 10 100 15 ; BB-BB-SC + 37 39 40 10 100 15 ; BB-BB-SC + 39 44 45 10 100 15 ; BB-BB-SC + 44 46 47 10 100 15 ; BB-BB-SC + 48 52 53 10 100 15 ; BB-BB-SC + 52 54 55 10 100 15 ; BB-BB-SC + 54 56 57 10 100 15 ; BB-BB-SC + 56 58 59 10 100 15 ; BB-BB-SC + 58 62 63 10 100 15 ; BB-BB-SC + 62 64 65 10 100 15 ; BB-BB-SC + 66 67 68 10 100 15 ; BB-BB-SC + 67 69 70 10 100 15 ; BB-BB-SC + 69 73 74 10 100 15 ; BB-BB-SC + 73 75 76 10 100 15 ; BB-BB-SC + 75 77 78 10 100 15 ; BB-BB-SC + 77 79 80 10 100 15 ; BB-BB-SC + 79 81 82 10 100 15 ; BB-BB-SC + 81 83 84 10 100 15 ; BB-BB-SC + 83 88 89 10 100 15 ; BB-BB-SC + 88 90 91 10 100 15 ; BB-BB-SC + 90 92 93 10 100 15 ; BB-BB-SC + 94 95 96 10 100 15 ; BB-BB-SC + 95 97 98 10 100 15 ; BB-BB-SC +100 101 102 10 100 15 ; BB-BB-SC +101 105 106 10 100 15 ; BB-BB-SC +105 109 110 10 100 15 ; BB-BB-SC +109 114 115 10 100 15 ; BB-BB-SC +114 116 117 10 100 15 ; BB-BB-SC +116 118 119 10 100 15 ; BB-BB-SC +118 121 122 10 100 15 ; BB-BB-SC + +; Side chain angles + 26 27 28 2 120.000 60.0 + 26 27 29 2 120.000 60.0 + 39 40 41 2 120.000 60.0 + 39 40 42 2 120.000 60.0 + 48 49 50 2 120.000 50.0 + 48 49 51 2 120.000 50.0 + 58 59 60 2 120.000 50.0 + 58 59 61 2 120.000 50.0 + 69 70 71 2 120.000 50.0 + 69 70 72 2 120.000 50.0 + 83 84 85 2 120.000 60.0 + 83 84 86 2 120.000 60.0 + 97 98 99 2 180.000 25.0 +101 102 103 2 120.000 50.0 +101 102 104 2 120.000 50.0 +105 106 107 2 120.000 50.0 +105 106 108 2 120.000 50.0 +109 110 111 2 120.000 60.0 +109 110 112 2 120.000 60.0 +118 119 120 2 180.000 25.0 + +[ dihedrals ] + 2 4 6 8 1 -120 400 1 + 4 6 8 10 1 -120 400 1 + 6 8 10 12 1 -120 400 1 + 24 26 31 33 1 -120 400 1 + 26 31 33 35 1 -120 400 1 + 67 69 73 75 1 -120 400 1 + 69 73 75 77 1 -120 400 1 + 73 75 77 79 1 -120 400 1 + 75 77 79 81 1 -120 400 1 + 77 79 81 83 1 -120 400 1 + 79 81 83 88 1 -120 400 1 + 81 83 88 90 1 -120 400 1 + 83 88 90 92 1 -120 400 1 + 88 90 92 94 1 -120 400 1 + 90 92 94 95 1 -120 400 1 + 92 94 95 97 1 -120 400 1 + +; SC-BB-BB-SC scFix + 3 2 4 5 1 -121.9 75 1 ; SC-BB-BB-SC + 5 4 6 7 1 -139.8 75 1 ; SC-BB-BB-SC + 7 6 8 9 1 126.7 75 1 ; SC-BB-BB-SC + 9 8 10 11 1 148.0 75 1 ; SC-BB-BB-SC + 11 10 12 13 1 -178.9 75 1 ; SC-BB-BB-SC + 13 12 14 15 1 -140.1 75 1 ; SC-BB-BB-SC + 15 14 16 17 1 141.7 75 1 ; SC-BB-BB-SC + 17 16 18 19 1 60.8 75 1 ; SC-BB-BB-SC + 19 18 20 21 1 42.9 75 1 ; SC-BB-BB-SC + 21 20 22 23 1 40.4 75 1 ; SC-BB-BB-SC + 23 22 24 25 1 63.0 75 1 ; SC-BB-BB-SC + 25 24 26 27 1 -99.1 75 1 ; SC-BB-BB-SC + 27 26 31 32 1 -144.6 75 1 ; SC-BB-BB-SC + 32 31 33 34 1 -133.4 75 1 ; SC-BB-BB-SC + 34 33 35 36 1 -151.0 75 1 ; SC-BB-BB-SC + 36 35 37 38 1 -119.2 75 1 ; SC-BB-BB-SC + 38 37 39 40 1 170.7 75 1 ; SC-BB-BB-SC + 40 39 44 45 1 111.2 75 1 ; SC-BB-BB-SC + 45 44 46 47 1 64.0 75 1 ; SC-BB-BB-SC + 49 48 52 53 1 -152.4 75 1 ; SC-BB-BB-SC + 53 52 54 55 1 169.6 75 1 ; SC-BB-BB-SC + 55 54 56 57 1 29.6 75 1 ; SC-BB-BB-SC + 57 56 58 59 1 51.8 75 1 ; SC-BB-BB-SC + 59 58 62 63 1 16.6 75 1 ; SC-BB-BB-SC + 63 62 64 65 1 22.2 75 1 ; SC-BB-BB-SC + 68 67 69 70 1 -146.5 75 1 ; SC-BB-BB-SC + 70 69 73 74 1 -168.2 75 1 ; SC-BB-BB-SC + 74 73 75 76 1 -120.4 75 1 ; SC-BB-BB-SC + 76 75 77 78 1 -117.0 75 1 ; SC-BB-BB-SC + 78 77 79 80 1 -122.0 75 1 ; SC-BB-BB-SC + 80 79 81 82 1 -153.2 75 1 ; SC-BB-BB-SC + 82 81 83 84 1 -124.4 75 1 ; SC-BB-BB-SC + 84 83 88 89 1 -144.2 75 1 ; SC-BB-BB-SC + 89 88 90 91 1 -148.1 75 1 ; SC-BB-BB-SC + 91 90 92 93 1 -158.9 75 1 ; SC-BB-BB-SC + 96 95 97 98 1 -124.4 75 1 ; SC-BB-BB-SC +102 101 105 106 1 25.9 75 1 ; SC-BB-BB-SC +106 105 109 110 1 -6.7 75 1 ; SC-BB-BB-SC +110 109 114 115 1 13.3 75 1 ; SC-BB-BB-SC +115 114 116 117 1 51.4 75 1 ; SC-BB-BB-SC +117 116 118 119 1 135.4 75 1 ; SC-BB-BB-SC +119 118 121 122 1 -159.0 75 1 ; SC-BB-BB-SC + 64 66 67 68 1 88.3 75 1 ; BB-BB-BB-SC + 65 64 66 67 1 -15.5 75 1 ; SC-BB-BB-BB + 92 94 95 96 1 68.7 75 1 ; BB-BB-BB-SC + 93 92 94 95 1 95.9 75 1 ; SC-BB-BB-BB + 97 100 101 102 1 -9.0 75 1 ; BB-BB-BB-SC + 98 97 100 101 1 74.1 75 1 ; SC-BB-BB-BB + +[ dihedrals ] + 30 28 29 27 2 180.0 50.0 + 43 41 42 40 2 180.0 50.0 + 87 85 86 84 2 180.0 50.0 +113 111 112 110 2 180.0 50.0 + +[ exclusions ] + 26 27 28 29 30 + 27 28 29 30 + 28 29 30 + 29 30 + 39 40 41 42 43 + 40 41 42 43 + 41 42 43 + 42 43 + 48 49 50 51 + 49 50 51 + 50 51 + 58 59 60 61 + 59 60 61 + 60 61 + 69 70 71 72 + 70 71 72 + 71 72 + 83 84 85 86 87 + 84 85 86 87 + 85 86 87 + 86 87 +101 102 103 104 +102 103 104 +103 104 +105 106 107 108 +106 107 108 +107 108 +109 110 111 112 113 +110 111 112 113 +111 112 113 +112 113 + diff --git a/vermouth/tests/helper_functions.py b/vermouth/tests/helper_functions.py index 3e44c81d9..37bea6f00 100644 --- a/vermouth/tests/helper_functions.py +++ b/vermouth/tests/helper_functions.py @@ -171,6 +171,21 @@ def parse_gofiles(file, atomtypes=False): vals[tup] = tuple((float(line[3]), float(line[4]))) return vals +def parse_enfiles(file): + ''' + Parser of en_bonds.itp files into an easy to assert dictionary + ''' + + with open(file) as f: + next(f) + next(f) # skip 2 header lines + vals = {} + for line in f: + line = line.split() + tup = tuple(sorted((line[0], line[1]))) + vals[tup] = tuple((int(line[2]), float(line[3]), float(line[4]))) + return vals + @pytest.fixture def test_molecule(scope='function'): """ diff --git a/vermouth/tests/integration_tests/test_integration.py b/vermouth/tests/integration_tests/test_integration.py index 63daf9f2f..09ab96cef 100644 --- a/vermouth/tests/integration_tests/test_integration.py +++ b/vermouth/tests/integration_tests/test_integration.py @@ -28,7 +28,7 @@ from vermouth.forcefield import ForceField from .. import datafiles -from ..helper_functions import find_in_path, parse_gofiles +from ..helper_functions import find_in_path, parse_gofiles, parse_enfiles INTEGRATION_DATA = Path(datafiles.TEST_DATA/'integration_tests') @@ -141,6 +141,21 @@ def compare_goatomtypes(fileref, filecomp): 'go_atomtypes.itp': compare_goatomtypes, 'virtual_sites_atomtypes.itp': compare_goatomtypes} +def compare_en(fileref, filecomp): + """ + Asserts that two en_bonds.itp files are functionally identical + """ + + ref = parse_enfiles(fileref) + compare = parse_enfiles(filecomp) + + assert set(ref.keys()) == set(compare.keys()) + + for key in ref.keys(): + assert ref[key] == compare[key] #assert correct atom definition string + +ENCOMPARERS = {'en_bonds.itp': compare_en} + def _interaction_equal(interaction1, interaction2): """ Returns True if interaction1 == interaction2, ignoring rounding errors in @@ -172,6 +187,7 @@ def _interaction_equal(interaction1, interaction2): ['tier-1', 'EN_chain'], ['tier-1', 'EN_region'], ['tier-1', 'hst5'], + ['tier-1', 'EN_ext'] # ['tier-2', 'barnase_barstar'], # ['tier-2', 'dna'], # ['tier-2', 'gpa_dimer'], @@ -240,6 +256,8 @@ def test_integration_protein(tmp_path, monkeypatch, tier, protein): if filename in GOCOMPARERS: # compare the extra go/vs model files GOCOMPARERS[filename](str(reference_file), str(new_file)) + elif filename in ENCOMPARERS: + ENCOMPARERS[filename](str(reference_file), str(new_file)) else: ext = new_file.suffix.lower() if ext in COMPARERS: diff --git a/vermouth/tests/test_apply_rubber_band.py b/vermouth/tests/test_apply_rubber_band.py index 5b9fc117d..85b8c4bcb 100644 --- a/vermouth/tests/test_apply_rubber_band.py +++ b/vermouth/tests/test_apply_rubber_band.py @@ -350,7 +350,8 @@ def test_apply_rubber_bands(test_molecule, chain_attribute, atom_names, res_min_ minimum_force=1, bond_type=6, domain_criterion=domain_criterion, - res_min_dist=res_min_dist) + res_min_dist=res_min_dist, + write_out=False) process.run_molecule(test_molecule) assert test_molecule.interactions['bonds'] == outcome @@ -424,7 +425,8 @@ def test_apply_rubber_bands_same_regions(test_molecule, regions, chain_attribute minimum_force=1, bond_type=6, domain_criterion=domain_criterion, - res_min_dist=res_min_dist) + res_min_dist=res_min_dist, + write_out=False) process.run_molecule(test_molecule) assert test_molecule.interactions['bonds'] == outcome @@ -449,7 +451,8 @@ def test_skip_no_matches(test_molecule): minimum_force=1, bond_type=6, domain_criterion=domain_criterion, - res_min_dist=3) + res_min_dist=3, + write_out=False) process.run_molecule(test_molecule) assert test_molecule.interactions['bonds'] == [] @@ -477,7 +480,8 @@ def test_bail_out_on_nan(caplog, test_molecule): minimum_force=1, bond_type=6, domain_criterion=domain_criterion, - res_min_dist=3) + res_min_dist=3, + write_out=False) process.run_molecule(test_molecule) required_warning = ("Found nan coordinates in molecule testmol. "