I am using this tutorial to generate parameters for an unkown residue I
have
http://ambermd.org/tutorials/basic/tutorial5/index.htm
I downloaded the .cif file from the pdb website
When I run this command I get this error
antechamber -fi ccif -i TYS.cif -bk TYS -fo ac -o tys.ac -c bcc -at gaff
syntax error near line 2
Target data block TYS is not in file
(I know -at gaff is not needed as gaff is default)
Many thanks
********************** The cif file************** (TYS.cif)
data_TYS
#
_chem_comp.id TYS
_chem_comp.name O-SULFO-L-TYROSINE
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C9 H11 N O6 S"
_chem_comp.mon_nstd_parent_comp_id TYR
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2012-11-26
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces STY
_chem_comp.formula_weight 261.252
_chem_comp.one_letter_code Y
_chem_comp.three_letter_code TYS
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
TYS N N N 0 1 N N N 16.013 1.950 -4.617 -3.373 1.476 -0.740 N TYS
1
TYS CA CA C 0 1 N N S 16.552 1.871 -3.258 -3.510 0.055 -0.396 CA TYS
2
TYS CB CB C 0 1 N N N 15.386 1.742 -2.268 -2.563 -0.284 0.757 CB TYS
3
TYS CG CG C 0 1 Y N N 14.473 2.961 -2.241 -1.136 -0.121 0.299 CG TYS
4
TYS CD1 CD1 C 0 1 Y N N 15.001 4.212 -1.950 -0.502 1.099 0.441 CD1 TYS
5
TYS CD2 CD2 C 0 1 Y N N 13.124 2.796 -2.486 -0.463 -1.192 -0.257 CD2 TYS
6
TYS CE1 CE1 C 0 1 Y N N 14.186 5.316 -1.930 0.806 1.252 0.023 CE1 TYS
7
TYS CE2 CE2 C 0 1 Y N N 12.300 3.899 -2.461 0.845 -1.045 -0.677 CE2 TYS
8
TYS CZ CZ C 0 1 Y N N 12.840 5.140 -2.179 1.482 0.180 -0.541 CZ TYS
9
TYS OH OH O 0 1 N N N 12.096 6.125 -2.152 2.768 0.327 -0.954 OH TYS
10
TYS S S S 0 1 N N N 11.372 6.454 -0.939 3.803 0.015 0.118 S TYS
11
TYS O1 O1 O 0 1 N N N 12.284 6.826 0.109 5.061 0.409 -0.412 O1 TYS
12
TYS O2 O2 O 0 1 N N N 10.523 5.390 -0.492 3.280 0.520 1.339 O2 TYS
13
TYS O3 O3 O 0 1 N N N 10.554 7.603 -1.197 3.855 -1.499 0.266 O3 TYS
14
TYS C C C 0 1 N N N 17.545 0.752 -2.992 -4.931 -0.226 0.023 C TYS
15
TYS O O O 0 1 N N N 18.218 0.693 -1.959 -5.645 0.680 0.381 O TYS
16
TYS OXT OXT O 0 1 N Y N 17.577 -0.181 -3.935 -5.402 -1.483 -0.004 OXT TYS
17
TYS H HN1 H 0 1 N N N 16.765 2.034 -5.270 -3.941 1.710 -1.541 H TYS
18
TYS HN2 HN2 H 0 1 N Y N 15.490 1.122 -4.817 -3.600 2.063 0.048 HN2 TYS
19
TYS HA HA H 0 1 N N N 17.061 2.821 -3.038 -3.260 -0.555 -1.263 HA TYS
20
TYS HB2 HB1 H 0 1 N N N 14.786 0.864 -2.549 -2.755 0.387 1.594 HB2 TYS
21
TYS HB3 HB2 H 0 1 N N N 15.800 1.595 -1.260 -2.728 -1.315 1.072 HB3 TYS
22
TYS HD1 HD1 H 0 1 N N N 16.055 4.316 -1.739 -1.028 1.934 0.880 HD1 TYS
23
TYS HD2 HD2 H 0 1 N N N 12.721 1.816 -2.694 -0.960 -2.146 -0.363 HD2 TYS
24
TYS HE1 HE1 H 0 1 N N N 14.588 6.297 -1.725 1.301 2.205 0.133 HE1 TYS
25
TYS HE2 HE2 H 0 1 N N N 11.243 3.796 -2.660 1.371 -1.883 -1.111 HE2 TYS
26
TYS HO3 HO3 H 0 1 N N N 10.813 8.313 -0.621 4.487 -1.808 0.929 HO3 TYS
27
TYS HXT HXT H 0 1 N Y N 18.183 -0.868 -3.681 -6.319 -1.613 0.273 HXT TYS
28
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
TYS N CA SING N N 1
TYS N H SING N N 2
TYS N HN2 SING N N 3
TYS CA CB SING N N 4
TYS CA C SING N N 5
TYS CA HA SING N N 6
TYS CB CG SING N N 7
TYS CB HB2 SING N N 8
TYS CB HB3 SING N N 9
TYS CG CD1 DOUB Y N 10
TYS CG CD2 SING Y N 11
TYS CD1 CE1 SING Y N 12
TYS CD1 HD1 SING N N 13
TYS CD2 CE2 DOUB Y N 14
TYS CD2 HD2 SING N N 15
TYS CE1 CZ DOUB Y N 16
TYS CE1 HE1 SING N N 17
TYS CE2 CZ SING Y N 18
TYS CE2 HE2 SING N N 19
TYS CZ OH SING N N 20
TYS OH S SING N N 21
TYS S O1 DOUB N N 22
TYS S O2 DOUB N N 23
TYS S O3 SING N N 24
TYS O3 HO3 SING N N 25
TYS C O DOUB N N 26
TYS C OXT SING N N 27
TYS OXT HXT SING N N 28
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
TYS SMILES ACDLabs 12.01
"O=C(O)C(N)Cc1ccc(OS(=O)(=O)O)cc1"
TYS InChI InChI 1.03
"InChI=1S/C9H11NO6S/c10-8(9(11)12)5-6-1-3-7(4-2-6)16-17(13,14)15/h1-4,8H,5,10H2,(H,11,12)(H,13,14,15)/t8-/m0/s1"
TYS InChIKey InChI 1.03
CIQHWLTYGMYQQR-QMMMGPOBSA-N
TYS SMILES_CANONICAL CACTVS 3.370
"N[C..H](Cc1ccc(O[S](O)(=O)=O)cc1)C(O)=O"
TYS SMILES CACTVS 3.370
"N[CH](Cc1ccc(O[S](O)(=O)=O)cc1)C(O)=O"
TYS SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6
"c1cc(ccc1C[C..H](C(=O)O)N)OS(=O)(=O)O"
TYS SMILES "OpenEye OEToolkits" 1.7.6
"c1cc(ccc1CC(C(=O)O)N)OS(=O)(=O)O"
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
TYS "SYSTEMATIC NAME" ACDLabs 12.01
O-sulfo-L-tyrosine
TYS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6
"(2S)-2-azanyl-3-(4-sulfooxyphenyl)propanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
TYS "Create component" 1999-07-08 EBI
TYS "Modify descriptor" 2011-06-04 RCSB
TYS "Modify leaving atom flag" 2012-11-26 RCSB
#
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Received on Mon Oct 08 2018 - 04:00:03 PDT
