Hi,
Does Anyone know why this error happened? Many thanks!
> On Sep 4, 2022, at 9:18 PM, Jiaan Zhu <zhujiaan16.mails.ucas.ac.cn> wrote:
>
> Dear David,
>
> I don’t know why my attachments are not shown in the mailing list. Maybe I need to paste them here:
> 1wa.prepin:
> 0 0 2
>
> This is a remark line
> molecule.res
> 1WA INT 0
> CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.523 111.21 .0 .00000
> 4 P P M 3 2 1 1.540 111.208 -180.000 1.763337
> 5 OP1 OH S 4 3 2 1.610 84.905 -44.040 -0.773614
> 6 HOP1 HO E 5 4 3 0.967 113.971 29.045 0.530369
> 7 OP2 O2 E 4 3 2 1.480 90.813 65.444 -0.883553
> 8 O5' OS M 4 3 2 1.611 148.273 -163.469 -0.607128
> 9 C5' CT M 8 4 3 1.429 122.953 -71.969 0.175675
> 10 H5' H1 E 9 8 4 1.090 109.443 60.048 0.076693
> 11 H5'A H1 E 9 8 4 1.090 109.509 -59.973 0.076693
> 12 C4' CT M 9 8 4 1.530 109.431 179.983 0.105466
> 13 O4' OS S 12 9 8 1.444 110.376 69.676 -0.444688
> 14 C1' CT 3 13 12 9 1.444 105.314 159.296 0.258143
> 15 N9 N2 S 14 13 12 1.465 110.409 -159.331 -0.063259
> 16 C4 CB S 15 14 13 1.321 125.681 -126.380 0.260777
> 17 N3 N2 B 16 15 14 1.386 132.293 -0.083 -0.292610
> 18 C2 CA B 17 16 15 1.359 118.958 -179.910 0.699864
> 19 N1 NC S 18 17 16 1.326 120.008 -0.038 -0.751015
> 20 C6 CA B 19 18 17 1.326 121.042 0.014 0.876451
> 21 N5 N2 S 20 19 18 1.341 120.903 0.060 -0.136387
> 22 C7 CA B 21 20 19 1.349 132.295 -179.960 -0.052601
> 23 C8 CA S 22 21 20 1.355 107.277 179.934 -0.086155
> 24 H8 H4 E 23 22 21 1.080 126.150 179.923 0.253280
> 25 H7 H4 E 22 21 20 1.080 126.357 -0.108 0.263411
> 26 O6 OH S 20 19 18 1.349 119.534 179.997 -0.492058
> 27 HO6 HO E 26 20 19 0.966 113.958 -0.004 0.539994
> 28 N2 N2 B 18 17 16 1.366 120.010 179.938 -0.401758
> 29 HN2 H E 28 18 17 0.970 119.970 -179.997 0.357834
> 30 HN2A H E 28 18 17 0.970 120.013 0.046 0.357834
> 31 HN3 H E 17 16 15 0.970 120.518 0.040 0.372525
> 32 C2' CT B 14 13 12 1.545 104.788 -40.472 -0.150400
> 33 H2' HC E 32 14 13 1.090 110.476 142.653 0.107593
> 34 H2'A HC E 32 14 13 1.090 110.484 -94.698 0.107593
> 35 H1' H2 E 14 13 12 1.091 110.331 78.446 0.138494
> 36 H4' H1 E 12 9 8 1.090 110.447 -52.645 0.142546
> 37 C3' CT M 12 9 8 1.545 110.390 -174.982 0.140925
> 38 H3' H1 E 37 12 9 1.090 110.462 -24.103 0.097969
> 39 O3' OH M 37 12 9 1.429 110.498 98.528 -0.568245
>
>
> LOOP
> C8 N9
> N5 C4
> C3' C2'
>
> IMPROPER
> C8 C4 N9 C1'
> N9 N3 C4 N5
> C2 C4 N3 HN3
> N3 N2 C2 N1
> N5 N1 C6 O6
> C6 C7 N5 C4
> C8 H7 C7 N5
> C7 H8 C8 N9
>
> DONE
> STOP
>
> 1wa.mc:
> HEAD_NAME P
> TAIL_NAME O3'
> MAIN_CHAIN O5'
> MAIN_CHAIN C5'
> MAIN_CHAIN C4'
> MAIN_CHAIN C3'
> OMIT_NAME OP3
> OMIT_NAME HOP3
> OMIT_NAME HO3'
> PRE_HEAD_TYPE O
> POST_TAIL_TYPE P
> CHARGE 2.0
>
> 1WA.cif:
> data_1WA
> #
> _chem_comp.id <http://chem_comp.id/> 1WA
> _chem_comp.name "2-amino-8-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-hydroxy-1H-imidazo[1,2-a][1,3,5]triazine-5,8-diium"
> _chem_comp.type "DNA"
> _chem_comp.pdbx_type ATOMN
> _chem_comp.formula "C10 H16 N5 O7 P"
> _chem_comp.mon_nstd_parent_comp_id ?
> _chem_comp.pdbx_synonyms ?
> _chem_comp.pdbx_formal_charge 2
> _chem_comp.pdbx_initial_date 2013-06-28
> _chem_comp.pdbx_modified_date 2015-05-22
> _chem_comp.pdbx_ambiguous_flag N
> _chem_comp.pdbx_release_status REL
> _chem_comp.pdbx_replaced_by ?
> _chem_comp.pdbx_replaces ?
> _chem_comp.formula_weight 349.237
> _chem_comp.one_letter_code ?
> _chem_comp.three_letter_code 1WA
> _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 4KZR
> _chem_comp.pdbx_subcomponent_list ?
> _chem_comp.pdbx_processing_site RCSB
> #
> 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
> 1WA OP3 OP3 O 0 1 N Y N 27.791 -5.608 13.760 -6.112 -0.098 0.377 OP3 1WA 1
> 1WA P P P 0 1 N N N 29.035 -5.748 12.812 -4.863 -1.108 0.268 P 1WA 2
> 1WA N1 N1 N 0 1 Y N N 22.149 -10.795 8.439 5.305 -0.796 0.703 N1 1WA 3
> 1WA C2 C2 C 0 1 Y N N 23.111 -11.725 8.406 4.610 -0.075 1.572 C2 1WA 4
> 1WA N2 N2 N 0 1 N N N 22.831 -12.914 7.803 5.153 0.242 2.785 N2 1WA 5
> 1WA N3 N3 N 0 1 Y N N 24.339 -11.364 8.827 3.358 0.349 1.256 N3 1WA 6
> 1WA C4 C4 C 0 1 Y N N 24.541 -10.155 9.403 2.829 0.016 0.019 C4 1WA 7
> 1WA N5 N5 N 1 1 Y N N 23.554 -9.235 9.502 3.568 -0.716 -0.833 N5 1WA 8
> 1WA C6 C6 C 0 1 Y N N 22.400 -9.546 8.922 4.799 -1.115 -0.480 C6 1WA 9
> 1WA O6 O6 O 0 1 N N N 21.288 -8.884 9.015 5.533 -1.850 -1.341 O6 1WA 10
> 1WA C7 C7 C 0 1 Y N N 24.142 -8.135 10.131 2.839 -0.904 -1.952 C7 1WA 11
> 1WA C8 C8 C 0 1 Y N N 25.345 -8.381 10.363 1.652 -0.277 -1.769 C8 1WA 12
> 1WA N9 N9 N 1 1 Y N N 25.645 -9.625 10.047 1.668 0.282 -0.552 N9 1WA 13
> 1WA "C1'" "C1'" C 0 1 N N R 26.902 -10.279 10.126 0.579 1.057 0.047 "C1'" 1WA 14
> 1WA "C2'" "C2'" C 0 1 N N N 27.713 -9.752 8.975 0.292 2.321 -0.794 "C2'" 1WA 15
> 1WA "C3'" "C3'" C 0 1 N N S 28.929 -9.027 9.639 -1.243 2.475 -0.729 "C3'" 1WA 16
> 1WA "O3'" "O3'" O 0 1 N N N 30.168 -9.379 9.060 -1.597 3.715 -0.113 "O3'" 1WA 17
> 1WA "C4'" "C4'" C 0 1 N N R 28.911 -9.375 11.098 -1.704 1.286 0.144 "C4'" 1WA 18
> 1WA "O4'" "O4'" O 0 1 N N N 27.577 -9.735 11.276 -0.653 0.304 0.013 "O4'" 1WA 19
> 1WA "C5'" "C5'" C 0 1 N N N 29.222 -8.403 12.228 -3.027 0.723 -0.378 "C5'" 1WA 20
> 1WA "O5'" "O5'" O 0 1 N N N 28.584 -7.167 12.069 -3.493 -0.296 0.509 "O5'" 1WA 21
> 1WA OP1 OP1 O 0 1 N N N 30.311 -5.774 13.605 -5.006 -2.261 1.383 OP1 1WA 22
> 1WA OP2 OP2 O 0 1 N N N 28.804 -4.601 11.962 -4.842 -1.723 -1.078 OP2 1WA 23
> 1WA HOP3 HOP3 H 0 0 N Y N 27.282 -4.848 13.505 -6.188 0.342 1.235 HOP3 1WA 24
> 1WA HN2 HN2 H 0 1 N N N 21.892 -12.901 7.460 6.047 -0.061 3.010 HN2 1WA 25
> 1WA HN2A HN2A H 0 0 N N N 23.462 -13.058 7.041 4.645 0.769 3.421 HN2A 1WA 26
> 1WA HN3 HN3 H 0 1 N N N 25.107 -11.994 8.713 2.843 0.877 1.886 HN3 1WA 27
> 1WA H7 H7 H 0 1 N N N 23.635 -7.214 10.379 3.145 -1.452 -2.831 H7 1WA 28
> 1WA H8 H8 H 0 1 N N N 26.047 -7.668 10.769 0.838 -0.234 -2.478 H8 1WA 29
> 1WA "H1'" "H1'" H 0 1 N N N 26.837 -11.377 10.130 0.828 1.330 1.073 "H1'" 1WA 30
> 1WA "H2'" "H2'" H 0 1 N N N 28.057 -10.577 8.334 0.783 3.190 -0.356 "H2'" 1WA 31
> 1WA "H2'A" "H2'A" H 0 0 N N N 27.121 -9.045 8.376 0.618 2.176 -1.824 "H2'A" 1WA 32
> 1WA "H3'" "H3'" H 0 1 N N N 28.768 -7.944 9.538 -1.677 2.406 -1.727 "H3'" 1WA 33
> 1WA "HO3'" "HO3'" H 0 0 N Y N 30.868 -8.911 9.500 -1.279 4.495 -0.588 "HO3'" 1WA 34
> 1WA "H4'" "H4'" H 0 1 N N N 29.547 -10.261 11.240 -1.806 1.596 1.184 "H4'" 1WA 35
> 1WA "H5'" "H5'" H 0 1 N N N 28.892 -8.850 13.177 -3.766 1.523 -0.432 "H5'" 1WA 36
> 1WA "H5'A" "H5'A" H 0 0 N N N 30.309 -8.236 12.260 -2.876 0.300 -1.371 "H5'A" 1WA 37
> 1WA HOP1 HOP1 H 0 0 N N N 30.813 -4.988 13.424 -5.810 -2.791 1.299 HOP1 1WA 38
> 1WA HO6 HO6 H 0 1 N N N 20.568 -9.431 8.724 6.406 -2.092 -1.005 HO6 1WA 39
> #
> 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
> 1WA P OP3 SING N N 1
> 1WA OP3 HOP3 SING N N 2
> 1WA OP2 P DOUB N N 3
> 1WA "O5'" P SING N N 4
> 1WA P OP1 SING N N 5
> 1WA C2 N1 DOUB Y N 6
> 1WA N1 C6 SING Y N 7
> 1WA N2 C2 SING N N 8
> 1WA C2 N3 SING Y N 9
> 1WA N2 HN2 SING N N 10
> 1WA N2 HN2A SING N N 11
> 1WA N3 C4 SING Y N 12
> 1WA N3 HN3 SING N N 13
> 1WA C4 N5 SING Y N 14
> 1WA C4 N9 DOUB Y N 15
> 1WA C6 N5 DOUB Y N 16
> 1WA N5 C7 SING Y N 17
> 1WA C6 O6 SING N N 18
> 1WA C7 C8 DOUB Y N 19
> 1WA C7 H7 SING N N 20
> 1WA N9 C8 SING Y N 21
> 1WA C8 H8 SING N N 22
> 1WA N9 "C1'" SING N N 23
> 1WA "C2'" "C1'" SING N N 24
> 1WA "C1'" "O4'" SING N N 25
> 1WA "C1'" "H1'" SING N N 26
> 1WA "C2'" "C3'" SING N N 27
> 1WA "C2'" "H2'" SING N N 28
> 1WA "C2'" "H2'A" SING N N 29
> 1WA "O3'" "C3'" SING N N 30
> 1WA "C3'" "C4'" SING N N 31
> 1WA "C3'" "H3'" SING N N 32
> 1WA "O3'" "HO3'" SING N N 33
> 1WA "C4'" "O4'" SING N N 34
> 1WA "C4'" "C5'" SING N N 35
> 1WA "C4'" "H4'" SING N N 36
> 1WA "O5'" "C5'" SING N N 37
> 1WA "C5'" "H5'" SING N N 38
> 1WA "C5'" "H5'A" SING N N 39
> 1WA OP1 HOP1 SING N N 40
> 1WA O6 HO6 SING N N 41
> #
> 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
> 1WA SMILES ACDLabs 12.01 "O=P(O)(O)OCC3OC([n+]2c1NC(=NC(O)=[n+]1cc2)N)CC3O"
> 1WA InChI InChI 1.03 "InChI=1S/C10H14N5O7P/c11-8-12-9-14(1-2-15(9)10(17)13-8)7-3-5(16)6(22-7)4-21-23(18,19)20/h1-2,5-7,16H,3-4H2,(H4,11,13,17,18,19,20)/p+2/t5-,6+,7+/m0/s1"
> 1WA InChIKey InChI 1.03 ZQGLFPASUDBGAQ-RRKCRQDMSA-P
> 1WA SMILES_CANONICAL CACTVS 3.385 "Nc1[nH]c2[n+](cc[n+]2c(O)n1)[C.H]3C[C.H](O)[C@@H](CO[P](O)(O)=O)O3"
> 1WA SMILES CACTVS 3.385 "Nc1[nH]c2[n+](cc[n+]2c(O)n1)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3"
> 1WA SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1c[n+]-2c(nc([nH]c2[n+]1[C.H]3C[C@@H]([C.H](O3)COP(=O)(O)O)O)N)O"
> 1WA SMILES "OpenEye OEToolkits" 1.7.6 "c1c[n+]-2c(nc([nH]c2[n+]1C3CC(C(O3)COP(=O)(O)O)O)N)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
> 1WA "SYSTEMATIC NAME" ACDLabs 12.01 "2-amino-8-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-hydroxy-1H-imidazo[1,2-a][1,3,5]triazine-5,8-diium"
> 1WA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-(2-azanyl-4-oxidanyl-1H-imidazo[1,2-a][1,3,5]triazine-5,8-diium-8-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
> #
> loop_
> _pdbx_chem_comp_audit.comp_id
> _pdbx_chem_comp_audit.action_type
> _pdbx_chem_comp_audit.date
> _pdbx_chem_comp_audit.processing_site
> 1WA "Create component" 2013-06-28 RCSB
> 1WA "Modify leaving atom flag" 2014-10-17 RCSB
> 1WA "Other modification" 2014-10-29 RCSB
> 1WA "Initial release" 2015-05-27 RCSB
> #
>
> Best regards,
> Jiaan
>
>> On Sep 4, 2022, at 3:04 PM, David A Case via AMBER <amber.ambermd.org <mailto:amber.ambermd.org>> wrote:
>>
>> On Sun, Sep 04, 2022, Jiaan Zhu via AMBER wrote:
>>>
>>> I’m trying to generate parameters of an artificial nucleotide by the following steps:
>>> 1. Download 1WA.cif file from PDB
>>> 2. antechamber -fi ccif -i 1WA.cif -bk 1WA -fo ac -o 1wa.ac -c bcc -at amber
>>> 3. prepgen -i 1wa.ac -o 1wa.prepin -m 1wa.mc -rn 1WA
>>> 4.parmchk2 -i 1wa.prepin -f prepi -o frcmod.1wa -a Y -p $AMBERHOME/dat/leap/parm/parm10.dat
>>>
>>> There’s an error in the step 4: $AMBERHOME/bin/parmchk2: line 4: 666869 Segmentation fault (core dumped) $AMBERHOME/bin/to_be_dispatched/parmchk2 "$@“
>>
>>> Does anyone know how to fix this problem? The 1WA.cif, 1wa.prepin and
>>> 1wa.mc files are attached.
>>
>> I don't see any attachments(?). It would be helpful to add the 1wa.prepin
>> file as well, since that is the actual input for the step that failed.
>>
>> ...thanks...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 22 2022 - 08:00:03 PDT
