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 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> 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
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Received on Sun Sep 04 2022 - 13:30:04 PDT
