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Opened 2 years ago
Closed 23 months ago
#9960 closed defect (fixed)
ChargeError during dockprep
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:\正在写的文章\CATH-2, PDLG, and GelMA-modified titanium surface modulates
> protein proteomic changes in LPS-activated
> macrophages\Fig\脂多糖结构\结构\LPS.mol2" format mol2
Opened LPS.mol2 containing 1 structures (604 atoms, 616 bonds)
> open "D:/正在写的文章/CATH-2, PDLG, and GelMA-modified titanium surface modulates
> protein proteomic changes in LPS-activated
> macrophages/Fig/CATH结构/预测的结构/selected_prediction.pdb"
Chain information for selected_prediction.pdb #2
---
Chain | Description
A | No description available
> ui tool show "Dock Prep"
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to multiple structures
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
37 hydrogen bonds
No usable SEQRES records for selected_prediction.pdb (#2) chain A; guessing
termini instead
Chain-initial residues that are actual N termini: selected_prediction.pdb #2/A
ARG 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: selected_prediction.pdb #2/A
PHE 26
Chain-final residues that are not actual C termini:
19 hydrogen bonds
2 hydrogens added
Closest equivalent command: addcharge standardizeResidues none
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue UNL (net charge +2) with am1-bcc method
Running ANTECHAMBER command: D:/ChimeraX/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
C:\Users\P70071~1\AppData\Local\Temp\tmptokijv1u\ante.in.mol2 -fi mol2 -o
C:\Users\P70071~1\AppData\Local\Temp\tmptokijv1u\ante.out.mol2 -fo mol2 -c bcc
-nc 2 -j 5 -s 2 -dr n
(UNL) ``
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`
(UNL) ``
(UNL) `Info: Finished reading file
(C:\Users\P70071~1\AppData\Local\Temp\tmptokijv1u\ante.in.mol2); atoms read
(606), bonds read (618).`
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNL) `Running: D:/ChimeraX/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) `Info: The number of bonds (512) exceeded MAXBOND.`
(UNL) ``
(UNL) ``
(UNL) `Running: D:/ChimeraX/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) `Info: The number of bonds (512) exceeded MAXBOND.`
(UNL) `Info: Total number of electrons: 2300; net charge: 2`
(UNL) ``
(UNL) `Running: D:/ChimeraX/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =839
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 1467
| QMMM: diag iterations used for timing = 1
| QMMM:
| QMMM: Internal diag routine = 7.738337 seconds
| QMMM: Dspev diag routine = 4.742490 seconds
| QMMM: Dspevd diag routine = 3.811492 seconds
| QMMM: Dspevx diag routine = ******** seconds
| QMMM: Dsyev diag routine = 4.622382 seconds
| QMMM: Dsyevd diag routine = 3.411181 seconds
| QMMM: Dsyevr diag routine = 3.074711 seconds
| QMMM:
| QMMM: Pseudo diag routine = 3.856437 seconds
| QMMM: Pseudo diagonalization appears to be slower than regular
| QMMM: diagonalization. Setting pseudo_diag=0 for optimum performance.
| QMMM:
| QMMM: Using dsyevr routine (diag_routine=7).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 P 3.7940 3.1020 -11.2470
QMMM: 2 2 P 2.1850 7.0320 -9.5080
QMMM: 3 3 P 0.8130 6.7500 0.3480
QMMM: 4 4 P 3.4650 1.8890 -13.7340
QMMM: 5 5 P 1.7460 -3.7150 -15.9200
QMMM: 6 6 P 3.6600 1.6930 -2.2660
QMMM: 7 7 O -2.7780 2.0170 -5.5710
QMMM: 8 8 O 0.6770 0.7570 -5.7850
QMMM: 9 9 O -1.0610 3.1740 -3.8670
QMMM: 10 10 O -3.3460 0.9960 -7.6010
QMMM: 11 11 O 2.5510 1.3200 -6.9070
QMMM: 12 12 O 0.1420 3.0920 -9.4570
QMMM: 13 13 O -2.0940 4.3060 -10.5100
QMMM: 14 14 O -0.8160 1.9620 -1.9350
QMMM: 15 15 O -1.9220 2.4000 -10.4650
QMMM: 16 16 O 2.8300 3.1840 -9.9530
QMMM: 17 17 O -0.7360 0.4860 -8.1260
QMMM: 18 18 O -1.5610 4.8660 -12.8140
QMMM: 19 19 O -2.9650 6.8640 -10.2690
QMMM: 20 20 O -5.5740 2.8480 -8.6130
QMMM: 21 21 O 2.1700 3.5500 -5.3310
QMMM: 22 22 O -2.0680 2.5640 0.4360
QMMM: 23 23 O -3.4170 8.9590 -10.5390
QMMM: 24 24 O -0.6600 5.7690 -8.8060
QMMM: 25 25 O -5.3620 4.4530 -10.8510
QMMM: 26 26 O 3.9490 3.8360 -7.5790
QMMM: 27 27 O -3.1990 -1.2560 -8.8690
QMMM: 28 28 O -2.7320 9.7420 -7.2510
QMMM: 29 29 O 1.4600 7.1320 -10.9990
QMMM: 30 30 O -0.4600 5.7710 0.0600
QMMM: 31 31 O -5.1790 3.2990 -5.4610
QMMM: 32 32 O -3.5010 1.7670 -1.6610
QMMM: 33 33 O -1.2260 5.6990 2.8680
QMMM: 34 34 O 1.2580 5.8080 -6.3750
QMMM: 35 35 O -0.5650 8.3650 -12.4610
QMMM: 36 36 O -0.3650 1.5690 1.5440
QMMM: 37 37 O -5.8110 1.2470 -6.1390
QMMM: 38 38 O -3.6940 3.4340 -3.1870
QMMM: 39 39 O -3.1880 3.3670 -13.8930
QMMM: 40 40 O -5.3150 7.7960 -8.7710
QMMM: 41 41 O -2.6310 11.9840 -7.1280
QMMM: 42 42 O -1.9680 0.5360 -12.5590
QMMM: 43 43 O -5.6780 10.1620 -9.3700
QMMM: 44 44 O 4.5170 2.6270 -5.4040
QMMM: 45 45 O -4.2520 -1.7990 -11.3150
QMMM: 46 46 O -3.7620 9.5400 -4.7740
QMMM: 47 47 O -3.3090 6.0140 -14.6170
QMMM: 48 48 O -0.6310 2.7130 -13.6060
QMMM: 49 49 O 3.0710 3.0590 -12.6900
QMMM: 50 50 O -1.3910 10.9090 -11.2630
QMMM: 51 51 O 0.3960 2.0040 -11.8390
QMMM: 52 52 O 4.4020 4.6150 -11.4780
QMMM: 53 53 O 5.0790 2.3740 -11.0970
QMMM: 54 54 O -0.4170 -0.2040 -13.9440
QMMM: 55 55 O 1.9390 0.0130 0.6550
QMMM: 56 56 O -4.9950 8.6600 -3.1890
QMMM: 57 57 O -5.0700 11.9440 -3.9060
QMMM: 58 58 O -1.4070 8.6970 -3.8880
QMMM: 59 59 O -0.8610 8.6190 -15.0510
QMMM: 60 60 O -3.2410 13.7270 -4.1460
QMMM: 61 61 O 3.6430 7.5000 -10.1420
QMMM: 62 62 O 0.6710 10.3310 -10.5710
QMMM: 63 63 O 1.6420 8.0050 -8.3620
QMMM: 64 64 O -0.7920 -1.2830 -1.3920
QMMM: 65 65 O 1.3670 -2.2740 -2.8070
QMMM: 66 66 O -1.6160 -1.8450 -10.9950
QMMM: 67 67 O 1.0360 -3.5230 -14.4800
QMMM: 68 68 O 1.7910 6.9780 -0.8930
QMMM: 69 69 O -0.1340 8.0460 0.6520
QMMM: 70 70 O 0.0530 8.7740 -2.1000
QMMM: 71 71 O 2.4100 5.6590 -8.9930
QMMM: 72 72 O -2.0380 5.7850 -3.5020
QMMM: 73 73 O -1.3080 -3.7630 -12.5720
QMMM: 74 74 O 2.9120 1.3100 -0.9100
QMMM: 75 75 O 1.4870 6.4690 1.6410
QMMM: 76 76 O -4.9840 5.5670 -3.9790
QMMM: 77 77 O -2.4090 1.5150 4.6980
QMMM: 78 78 O -0.2400 13.2450 -6.9190
QMMM: 79 79 O -2.3930 7.3410 1.7750
QMMM: 80 80 O 0.5380 10.6730 -13.3390
QMMM: 81 81 O 4.4840 0.7180 -13.3300
QMMM: 82 82 O 1.9350 13.5010 -11.5710
QMMM: 83 83 O -1.4910 -0.5990 -16.2710
QMMM: 84 84 O 1.9270 1.4070 -13.9460
QMMM: 85 85 O -5.1010 0.4610 4.9340
QMMM: 86 86 O 3.9030 11.9250 -10.9490
QMMM: 87 87 O 0.7060 10.9070 -4.9150
QMMM: 88 88 O 3.7990 2.5100 -15.0450
QMMM: 89 89 O -3.7810 8.1300 4.4080
QMMM: 90 90 O -3.7380 7.8410 -0.4920
QMMM: 91 91 O 2.7710 9.5610 -2.2600
QMMM: 92 92 O 0.2340 1.4880 -16.0640
QMMM: 93 93 O 1.1070 10.8650 -7.9340
QMMM: 94 94 O -0.2190 12.3640 -1.6130
QMMM: 95 95 O 2.7540 -2.6020 -16.4390
QMMM: 96 96 O 2.5270 -5.1030 -15.5670
QMMM: 97 97 O 4.0520 -3.6250 -2.1500
QMMM: 98 98 O 0.8070 -4.1990 -16.9630
QMMM: 99 99 O 3.5350 3.2570 -2.7080
QMMM: 100 100 O 2.9080 1.2560 -3.6280
QMMM: 101 101 O 2.7270 -1.2630 -4.3590
QMMM: 102 102 O 5.1140 1.4200 -2.3460
QMMM: 103 103 O 3.0630 7.8400 -6.0690
QMMM: 104 104 O 6.7120 -0.7800 -2.0920
QMMM: 105 105 O 3.1450 -2.6290 -6.6770
QMMM: 106 106 O -4.3550 -1.1920 6.3400
QMMM: 107 107 O -4.2720 5.9930 3.7580
QMMM: 108 108 N -2.8060 3.4150 3.5470
QMMM: 109 109 N 4.0730 -1.3590 -2.0860
QMMM: 110 110 N 2.1050 7.6790 -4.0350
QMMM: 111 111 N 5.4570 5.5020 -9.1590
QMMM: 112 112 N 3.7920 -0.7730 -10.8810
QMMM: 113 113 C -0.3120 1.7640 -5.6650
QMMM: 114 114 C -1.6980 1.1330 -5.3860
QMMM: 115 115 C 0.0790 2.7320 -4.5350
QMMM: 116 116 C -1.6930 0.8460 -3.8740
QMMM: 117 117 C -3.5660 2.0970 -6.7640
QMMM: 118 118 C -1.6340 2.1570 -3.0720
QMMM: 119 119 C 0.9680 2.3070 -8.6450
QMMM: 120 120 C 1.3660 0.5470 -7.0210
QMMM: 121 121 C -3.1760 3.3450 -9.2870
QMMM: 122 122 C 0.6000 0.8520 -8.2950
QMMM: 123 123 C -3.1630 3.3650 -7.5670
QMMM: 124 124 C 2.3590 2.0570 -9.2730
QMMM: 125 125 C -4.4800 2.2820 -9.3450
QMMM: 126 126 C 3.2610 1.5690 -8.1070
QMMM: 127 127 C -4.2280 0.9100 -8.6820
QMMM: 128 128 C 0.9050 3.9630 -4.8870
QMMM: 129 129 C -1.2260 3.2240 -9.1700
QMMM: 130 130 C -3.2470 5.6390 -9.6770
QMMM: 131 131 C -1.8120 4.9710 -8.7470
QMMM: 132 132 C -1.0040 4.1700 -11.6760
QMMM: 133 133 C -3.9680 4.5740 -11.0220
QMMM: 134 134 C -3.1610 2.9770 -11.4100
QMMM: 135 135 C 4.4170 2.5210 -7.7730
QMMM: 136 136 C -3.7450 -0.1920 -9.6160
QMMM: 137 137 C 0.3070 4.9960 -11.4410
QMMM: 138 138 C -1.3610 3.6060 -0.1920
QMMM: 139 139 C -4.9880 2.1380 -6.1280
QMMM: 140 140 C -3.0570 2.5490 -2.6660
QMMM: 141 141 C -0.3730 3.1020 -1.2330
QMMM: 142 142 C 0.2400 6.5120 -11.3200
QMMM: 143 143 C -1.5710 6.2700 -12.9890
QMMM: 144 144 C 0.2900 4.8940 -5.9110
QMMM: 145 145 C -0.2760 6.9990 -12.6470
QMMM: 146 146 C -0.6520 4.5720 0.7650
QMMM: 147 147 C -1.5940 4.7110 1.9510
QMMM: 148 148 C -3.0280 8.0600 -9.5120
QMMM: 149 149 C -3.4640 2.4560 -12.8590
QMMM: 150 150 C -1.6160 3.3600 2.6870
QMMM: 151 151 C -4.0100 8.1310 -8.3510
QMMM: 152 152 C -4.0140 9.5530 -7.7870
QMMM: 153 153 C -1.6320 2.1750 1.7160
QMMM: 154 154 C -4.3640 10.4760 -8.9530
QMMM: 155 155 C 5.2220 2.1610 -6.5350
QMMM: 156 156 C -4.8210 -0.7810 -10.5120
QMMM: 157 157 C -3.4560 10.3060 -10.1650
QMMM: 158 158 C -2.0210 6.5630 -14.4320
QMMM: 159 159 C -0.3540 2.8430 -12.2890
QMMM: 160 160 C -3.0620 1.0340 -13.2870
QMMM: 161 161 C -2.4900 10.8150 -6.3650
QMMM: 162 162 C -3.2780 10.8220 -5.0660
QMMM: 163 163 C -2.0780 10.9400 -10.0340
QMMM: 164 164 C -4.3660 11.8790 -5.1240
QMMM: 165 165 C -2.1310 8.0270 -14.8520
QMMM: 166 166 C -3.7220 13.2380 -5.3770
QMMM: 167 167 C -2.5880 13.1770 -6.4040
QMMM: 168 168 C -0.4220 0.2160 1.1230
QMMM: 169 169 C 0.6600 -0.0450 0.0800
QMMM: 170 170 C -1.4380 -0.6640 -13.0940
QMMM: 171 171 C -3.6840 9.1540 -3.4070
QMMM: 172 172 C -2.5360 8.1610 -3.2310
QMMM: 173 173 C 0.4850 -1.2820 -0.7950
QMMM: 174 174 C -0.7590 -1.5110 -12.0530
QMMM: 175 175 C -3.1130 2.4690 4.4810
QMMM: 176 176 C -2.9820 6.8010 -3.7460
QMMM: 177 177 C 1.5340 -1.2200 -1.9040
QMMM: 178 178 C -0.3010 -2.7880 -12.7280
QMMM: 179 179 C 0.2190 -1.1960 -14.7090
QMMM: 180 180 C -0.0260 -2.6340 -14.2300
QMMM: 181 181 C 2.9040 -1.2040 -1.2090
QMMM: 182 182 C -4.2600 6.3520 -3.0510
QMMM: 183 183 C -1.7450 6.9510 2.7200
QMMM: 184 184 C -0.0700 11.3920 -11.1300
QMMM: 185 185 C -5.1190 7.4680 -2.4770
QMMM: 186 186 C -1.1830 13.4410 -5.8810
QMMM: 187 187 C 2.9900 0.0300 -0.3010
QMMM: 188 188 C 0.5230 11.7800 -12.4660
QMMM: 189 189 C -4.4340 2.7210 5.1930
QMMM: 190 190 C -0.1550 8.2720 -3.3990
QMMM: 191 191 C -1.4390 7.8090 3.9370
QMMM: 192 192 C 1.9460 12.2620 -12.2390
QMMM: 193 193 C -0.1160 -0.8850 -16.1720
QMMM: 194 194 C 0.9930 8.5840 -4.3540
QMMM: 195 195 C 2.7270 11.2850 -11.3790
QMMM: 196 196 C 1.9540 10.7330 -10.1860
QMMM: 197 197 C -5.0120 1.4810 5.8900
QMMM: 198 198 C 1.5460 10.0020 -4.2520
QMMM: 199 199 C -5.0570 7.6680 -0.9590
QMMM: 200 200 C -2.5580 7.7650 4.9880
QMMM: 201 201 C 1.7340 10.3610 -2.7920
QMMM: 202 202 C 0.4900 10.0970 -1.9650
QMMM: 203 203 C -6.4000 1.7860 6.4690
QMMM: 204 204 C 0.6390 0.3100 -16.7350
QMMM: 205 205 C 4.7270 7.8690 -9.3280
QMMM: 206 206 C -2.2600 8.7280 6.1450
QMMM: 207 207 C 1.9230 11.5330 -8.8870
QMMM: 208 208 C -0.6330 11.1060 -2.1070
QMMM: 209 209 C 4.5600 -2.5810 -2.4740
QMMM: 210 210 C -7.0140 0.6070 7.2430
QMMM: 211 211 C 2.0020 -2.1710 -4.0160
QMMM: 212 212 C -3.3050 8.6560 7.2720
QMMM: 213 213 C 5.2340 6.7510 -8.4200
QMMM: 214 214 C 5.7740 -2.5170 -3.3900
QMMM: 215 215 C -8.3870 0.9660 7.8340
QMMM: 216 216 C 4.1010 -0.6340 -13.3330
QMMM: 217 217 C 1.7290 -3.3840 -4.8920
QMMM: 218 218 C -2.9940 9.6390 8.4130
QMMM: 219 219 C 3.0780 7.3900 -4.9500
QMMM: 220 220 C 7.0230 -2.0260 -2.6610
QMMM: 221 221 C -4.6620 -0.7950 5.2390
QMMM: 222 222 C -9.0170 -0.2170 8.5880
QMMM: 223 223 C 2.9290 -3.7030 -5.7900
QMMM: 224 224 C -4.5590 7.1650 3.8370
QMMM: 225 225 C -4.0760 9.6100 9.5050
QMMM: 226 226 C 3.1550 -0.9940 -12.1890
QMMM: 227 227 C 8.2210 -1.8770 -3.6000
QMMM: 228 228 C -4.6100 -1.6280 3.9660
QMMM: 229 229 C -10.3950 0.1400 9.1670
QMMM: 230 230 C 4.1540 6.4590 -4.4320
QMMM: 231 231 C 2.7600 -4.9990 -6.5850
QMMM: 232 232 C -5.8400 7.7830 3.2990
QMMM: 233 233 C -3.7960 10.6250 10.6240
QMMM: 234 234 C 9.4990 -1.4350 -2.8690
QMMM: 235 235 C -4.2710 -3.1070 4.2080
QMMM: 236 236 C -11.0300 -1.0430 9.9160
QMMM: 237 237 C 4.0410 -5.3740 -7.3500
QMMM: 238 238 C -6.9160 6.7410 2.9600
QMMM: 239 239 C -4.9040 10.6240 11.6890
QMMM: 240 240 C 10.7080 -1.3440 -3.8140
QMMM: 241 241 C -4.2640 -3.9190 2.9030
QMMM: 242 242 C -12.4110 -0.6850 10.4900
QMMM: 243 243 C 3.9560 -6.7660 -7.9990
QMMM: 244 244 C -8.2320 7.4010 2.5180
QMMM: 245 245 C -4.6440 11.6620 12.7940
QMMM: 246 246 C 11.9750 -0.8870 -3.0720
QMMM: 247 247 C -3.9520 -5.4030 3.1560
QMMM: 248 248 C 5.2780 -7.1490 -8.6850
QMMM: 249 249 C -13.0470 -1.8670 11.2390
QMMM: 250 250 C -9.3430 6.3630 2.2840
QMMM: 251 251 C -5.7680 11.6770 13.8430
QMMM: 252 252 C 13.1910 -0.7860 -4.0070
QMMM: 253 253 C -3.9720 -6.2300 1.8600
QMMM: 254 254 C 5.2530 -8.5810 -9.2450
QMMM: 255 255 C -14.4280 -1.5080 11.8120
QMMM: 256 256 C -10.6850 7.0270 1.9350
QMMM: 257 257 C -5.5190 12.7260 14.9390
QMMM: 258 258 C 14.4500 -0.3190 -3.2570
QMMM: 259 259 C -3.6820 -7.7160 2.1260
QMMM: 260 260 C 6.6040 -8.9700 -9.8690
QMMM: 261 261 C -11.8160 5.9960 1.7880
QMMM: 262 262 C -15.0650 -2.6880 12.5620
QMMM: 263 263 C -6.6490 12.7490 15.9810
QMMM: 264 264 C 15.6700 -0.2090 -4.1850
QMMM: 265 265 C -3.7210 -8.5530 0.8370
QMMM: 266 266 C 6.6160 -10.4230 -10.3700
QMMM: 267 267 C -13.1700 6.6660 1.5050
QMMM: 268 268 C 16.9230 0.2640 -3.4300
QMMM: 269 269 C -3.4430 -10.0400 1.1110
QMMM: 270 270 C -16.4430 -2.3250 13.1320
QMMM: 271 271 C 7.9820 -10.8140 -10.9570
QMMM: 272 272 C -14.3120 5.6410 1.4160
QMMM: 273 273 C -6.4000 13.8000 17.0700
QMMM: 274 274 C 18.1450 0.3800 -4.3550
QMMM: 275 275 C -3.4910 -10.8830 -0.1740
QMMM: 276 276 C 8.0140 -12.2780 -11.4250
QMMM: 277 277 C -15.6720 6.3150 1.1720
QMMM: 278 278 C 19.3950 0.8570 -3.5990
QMMM: 279 279 C -16.8190 5.2930 1.1140
QMMM: 280 280 C -3.2170 -12.3700 0.1030
QMMM: 281 281 C 9.3850 -12.6690 -11.9990
QMMM: 282 282 C -18.1810 5.9700 0.8890
QMMM: 283 283 C 20.6130 0.9730 -4.5250
QMMM: 284 284 C -3.2680 -13.2090 -1.1810
QMMM: 285 285 C 9.4190 -14.1340 -12.4530
QMMM: 286 286 C -19.3300 4.9500 0.8420
QMMM: 287 287 C -20.6880 5.6300 0.6230
QMMM: 288 288 H -0.3930 2.3480 -6.5850
QMMM: 289 289 H -1.8730 0.1790 -5.9270
QMMM: 290 290 H 0.6980 2.1790 -3.7930
QMMM: 291 291 H -0.8170 0.1950 -3.6470
QMMM: 292 292 H -2.5860 0.2410 -3.5920
QMMM: 293 293 H 1.1490 2.9610 -7.7660
QMMM: 294 294 H 1.6710 -0.5250 -7.0260
QMMM: 295 295 H -4.0260 4.0180 -9.1310
QMMM: 296 296 H 0.9070 0.1410 -9.0990
QMMM: 297 297 H -2.2160 3.5770 -7.0340
QMMM: 298 298 H -3.8070 4.1860 -7.1600
QMMM: 299 299 H 2.2820 1.2660 -10.0550
QMMM: 300 300 H -5.1290 2.0940 -10.2310
QMMM: 301 301 H 3.7180 0.5930 -8.4050
QMMM: 302 302 H -5.1920 0.4970 -8.3040
QMMM: 303 303 H 1.0950 4.5590 -3.9600
QMMM: 304 304 H -1.3220 2.5340 -8.3310
QMMM: 305 305 H -4.0760 5.8500 -8.9650
QMMM: 306 306 H -2.0590 5.2900 -7.7080
QMMM: 307 307 H -3.9250 5.1730 -11.9640
QMMM: 308 308 H -3.7490 2.0750 -11.2030
QMMM: 309 309 H 5.1320 2.5580 -8.6230
QMMM: 310 310 H -2.9120 0.2010 -10.2260
QMMM: 311 311 H 0.9850 4.8220 -12.3150
QMMM: 312 312 H 0.9420 4.6440 -10.6240
QMMM: 313 313 H -2.1420 4.1830 -0.7500
QMMM: 314 314 H -0.0350 3.9180 -1.9020
QMMM: 315 315 H 0.5710 2.8180 -0.7210
QMMM: 316 316 H -0.5090 6.8890 -10.6040
QMMM: 317 317 H -2.3760 6.6850 -12.3550
QMMM: 318 318 H -0.5620 5.4770 -5.5040
QMMM: 319 319 H -0.0660 4.3510 -6.8000
QMMM: 320 320 H 0.4880 6.9000 -13.4490
QMMM: 321 321 H 0.3270 4.1590 1.0970
QMMM: 322 322 H -2.6250 4.9180 1.5790
QMMM: 323 323 H -1.9920 8.2910 -9.1810
QMMM: 324 324 H -4.5920 2.4530 -12.9630
QMMM: 325 325 H -0.7130 3.2830 3.3410
QMMM: 326 326 H -1.2200 0.3820 -8.9470
QMMM: 327 327 H -3.7290 7.4310 -7.5290
QMMM: 328 328 H -4.7770 9.6260 -6.9820
QMMM: 329 329 H -2.3460 1.4100 2.0990
QMMM: 330 330 H -6.0130 3.5180 -9.1430
QMMM: 331 331 H -4.4210 11.5440 -8.6510
QMMM: 332 332 H 6.2060 2.6830 -6.5340
QMMM: 333 333 H 5.3860 1.0660 -6.4310
QMMM: 334 334 H -5.2660 -0.0250 -11.1930
QMMM: 335 335 H -5.6350 -1.2520 -9.9170
QMMM: 336 336 H -3.9460 10.8390 -11.0210
QMMM: 337 337 H 2.2850 2.5940 -5.2870
QMMM: 338 338 H -1.3490 6.0290 -15.1440
QMMM: 339 339 H -2.8200 1.0230 -14.3740
QMMM: 340 340 H -3.9140 0.3320 -13.1330
QMMM: 341 341 H -0.8700 6.7030 -8.7820
QMMM: 342 342 H -5.8080 5.1890 -11.2730
QMMM: 343 343 H -1.4070 10.7050 -6.1240
QMMM: 344 344 H 3.6070 4.2530 -8.3750
QMMM: 345 345 H -2.5740 11.1400 -4.2690
QMMM: 346 346 H -2.7560 -1.8500 -9.4820
QMMM: 347 347 H -3.4490 4.1940 3.4140
QMMM: 348 348 H -1.4610 10.4370 -9.2640
QMMM: 349 349 H -2.2090 12.0070 -9.7370
QMMM: 350 350 H -4.3390 3.7560 -5.2830
QMMM: 351 351 H -2.7670 1.2910 -1.2370
QMMM: 352 352 H -5.1040 11.6360 -5.9220
QMMM: 353 353 H 1.9140 5.3440 -6.9070
QMMM: 354 354 H 0.2170 8.9090 -12.3350
QMMM: 355 355 H -2.6890 8.6320 -14.1040
QMMM: 356 356 H -2.6650 8.1090 -15.8270
QMMM: 357 357 H -4.5130 13.9560 -5.7000
QMMM: 358 358 H -2.7830 13.9800 -7.1620
QMMM: 359 359 H -2.2610 3.5930 -13.9350
QMMM: 360 360 H -0.2970 -0.4470 2.0090
QMMM: 361 361 H -1.4130 -0.0010 0.6660
QMMM: 362 362 H -5.9640 8.2910 -8.2650
QMMM: 363 363 H 0.5750 0.8010 -0.6220
QMMM: 364 364 H -2.2180 -1.2270 -13.6480
QMMM: 365 365 H -3.5520 10.0300 -2.7340
QMMM: 366 366 H -5.6310 9.4170 -9.9790
QMMM: 367 367 H 4.0740 3.4460 -5.6540
QMMM: 368 368 H -2.2830 8.0710 -2.1580
QMMM: 369 369 H -4.9510 -2.2810 -11.7620
QMMM: 370 370 H 0.5630 -2.2140 -0.1920
QMMM: 371 371 H -3.2550 5.0610 -14.6540
QMMM: 372 372 H 0.0940 -0.9530 -11.6010
QMMM: 373 373 H -0.2120 1.9070 -13.9470
QMMM: 374 374 H -3.1160 6.8640 -4.8510
QMMM: 375 375 H 1.3510 -0.2790 -2.4690
QMMM: 376 376 H 0.5860 -3.1730 -12.1720
QMMM: 377 377 H 1.3130 -1.0280 -14.5690
QMMM: 378 378 H -0.9140 -3.0050 -14.7990
QMMM: 379 379 H 2.9250 -2.0750 -0.5050
QMMM: 380 380 H -4.0230 5.6800 -2.1950
QMMM: 381 381 H -0.0830 12.2740 -10.4550
QMMM: 382 382 H 5.3170 4.6210 -11.2530
QMMM: 383 383 H -6.1890 7.1680 -2.6370
QMMM: 384 384 H -0.9110 12.7730 -5.0400
QMMM: 385 385 H -1.0770 14.4930 -5.5330
QMMM: 386 386 H 3.9500 -0.0060 0.2690
QMMM: 387 387 H -0.0900 12.5690 -12.9580
QMMM: 388 388 H -4.2730 3.5430 5.9300
QMMM: 389 389 H -5.1690 3.0830 4.4350
QMMM: 390 390 H -0.1870 7.1630 -3.3030
QMMM: 391 391 H -4.5750 12.4980 -3.2960
QMMM: 392 392 H -0.4680 7.4950 4.3850
QMMM: 393 393 H -1.3000 8.8570 3.5820
QMMM: 394 394 H 2.4640 12.4360 -13.2110
QMMM: 395 395 H 0.0670 -1.7580 -16.8320
QMMM: 396 396 H 0.6400 8.3820 -5.3950
QMMM: 397 397 H -0.6190 9.1130 -14.2630
QMMM: 398 398 H -2.9590 14.6390 -4.2390
QMMM: 399 399 H 3.0460 10.4340 -12.0290
QMMM: 400 400 H 2.4950 9.7990 -9.9100
QMMM: 401 401 H -4.3160 1.2050 6.7150
QMMM: 402 402 H 2.5220 10.0970 -4.7850
QMMM: 403 403 H -5.4560 6.7740 -0.4260
QMMM: 404 404 H -5.6470 8.5530 -0.6320
QMMM: 405 405 H -2.6240 6.7390 5.4200
QMMM: 406 406 H 2.0730 11.4180 -2.6910
QMMM: 407 407 H 4.4830 -0.5270 -2.5140
QMMM: 408 408 H 0.8010 10.1840 -0.8900
QMMM: 409 409 H 1.7890 7.6180 -7.5090
QMMM: 410 410 H -0.8770 -2.0630 -1.9460
QMMM: 411 411 H -2.3360 -2.3850 -11.3360
QMMM: 412 412 H 1.7280 7.8650 -1.2000
QMMM: 413 413 H -1.0400 7.8480 0.4640
QMMM: 414 414 H -2.4140 4.9240 -3.7250
QMMM: 415 415 H -0.9720 -4.6250 -12.8250
QMMM: 416 416 H -7.0900 2.0810 5.6430
QMMM: 417 417 H -6.3180 2.6610 7.1570
QMMM: 418 418 H 0.4170 0.4490 -17.8170
QMMM: 419 419 H 1.7380 0.2040 -16.6110
QMMM: 420 420 H -5.0400 4.6550 -3.6830
QMMM: 421 421 H 5.5490 8.1800 -10.0150
QMMM: 422 422 H 4.4420 8.7630 -8.7260
QMMM: 423 423 H -2.2140 9.7710 5.7500
QMMM: 424 424 H -1.2560 8.4920 6.5710
QMMM: 425 425 H 1.5360 12.5660 -9.0120
QMMM: 426 426 H 2.9430 11.6050 -8.4460
QMMM: 427 427 H -0.2280 12.3220 -7.1910
QMMM: 428 428 H 2.2400 7.4250 -3.0530
QMMM: 429 429 H 0.6800 10.9700 -14.2410
QMMM: 430 430 H -1.5350 10.8070 -1.5270
QMMM: 431 431 H -0.9160 11.2650 -3.1620
QMMM: 432 432 H -7.1340 -0.2680 6.5620
QMMM: 433 433 H -6.3240 0.3030 8.0650
QMMM: 434 434 H 2.8300 13.6790 -11.2660
QMMM: 435 435 H -1.6030 0.3080 -15.9670
QMMM: 436 436 H 1.5480 1.1660 -13.1240
QMMM: 437 437 H -3.3460 7.6170 7.6770
QMMM: 438 438 H -4.3170 8.8930 6.8650
QMMM: 439 439 H 4.5260 11.2830 -10.6040
QMMM: 440 440 H 0.9270 10.9420 -5.8490
QMMM: 441 441 H 4.5090 6.5290 -7.6100
QMMM: 442 442 H 6.1860 7.0580 -7.9260
QMMM: 443 443 H -3.6750 7.7480 0.4630
QMMM: 444 444 H 5.9680 -3.5300 -3.8160
QMMM: 445 445 H 5.5310 -1.8440 -4.2450
QMMM: 446 446 H 3.2020 10.0250 -1.5390
QMMM: 447 447 H -8.2770 1.8310 8.5300
QMMM: 448 448 H -9.0710 1.2840 7.0110
QMMM: 449 449 H 3.6590 -0.8890 -14.3230
QMMM: 450 450 H 5.0350 -1.2360 -13.2310
QMMM: 451 451 H 1.5120 -4.2650 -4.2440
QMMM: 452 452 H 0.8250 -3.1750 -5.5100
QMMM: 453 453 H -2.9210 10.6720 7.9970
QMMM: 454 454 H -2.0030 9.3890 8.8610
QMMM: 455 455 H 0.9900 1.8790 -15.6170
QMMM: 456 456 H 7.2720 -2.7170 -1.8230
QMMM: 457 457 H 1.0950 9.9240 -8.1330
QMMM: 458 458 H -9.1220 -1.0840 7.8930
QMMM: 459 459 H -8.3370 -0.5320 9.4150
QMMM: 460 460 H 3.8400 -3.7840 -5.1530
QMMM: 461 461 H -5.0670 9.8370 9.0450
QMMM: 462 462 H -4.1370 8.5840 9.9390
QMMM: 463 463 H 2.8860 -2.0730 -12.2660
QMMM: 464 464 H 2.2060 -0.4200 -12.2280
QMMM: 465 465 H -0.8900 13.0190 -1.8170
QMMM: 466 466 H 2.5540 -2.3910 -17.3350
QMMM: 467 467 H 2.1680 -5.7830 -16.1110
QMMM: 468 468 H 7.9760 -1.1400 -4.4010
QMMM: 469 469 H 8.4100 -2.8580 -4.0990
QMMM: 470 470 H 5.7750 4.7630 -8.5070
QMMM: 471 471 H 4.5470 5.1690 -9.5230
QMMM: 472 472 H -5.6040 -1.5590 3.4620
QMMM: 473 473 H -3.8450 -1.1780 3.2900
QMMM: 474 474 H 4.8510 6.1500 -5.2420
QMMM: 475 475 H 4.7410 6.9630 -3.6320
QMMM: 476 476 H 3.6910 5.5380 -4.0120
QMMM: 477 477 H -11.0720 0.4580 8.3380
QMMM: 478 478 H -10.2910 1.0060 9.8630
QMMM: 479 479 H 1.9050 -4.9020 -7.2930
QMMM: 480 480 H 2.5130 -5.8230 -5.8740
QMMM: 481 481 H 3.4260 3.2990 -3.6460
QMMM: 482 482 H 3.3940 0.6220 -4.1260
QMMM: 483 483 H -6.2420 8.4880 4.0650
QMMM: 484 484 H -5.5820 8.3700 2.3860
QMMM: 485 485 H -2.8160 10.3890 11.1040
QMMM: 486 486 H -3.7130 11.6470 10.1820
QMMM: 487 487 H 9.7250 -2.1590 -2.0500
QMMM: 488 488 H 9.3350 -0.4380 -2.3970
QMMM: 489 489 H -3.2690 -3.1850 4.6940
QMMM: 490 490 H -5.0210 -3.5460 4.9090
QMMM: 491 491 H -11.1330 -1.9090 9.2200
QMMM: 492 492 H -10.3550 -1.3590 10.7460
QMMM: 493 493 H 4.9030 -5.3630 -6.6410
QMMM: 494 494 H 4.2490 -4.6110 -8.1370
QMMM: 495 495 H -6.5500 6.0670 2.1490
QMMM: 496 496 H -7.1070 6.1120 3.8620
QMMM: 497 497 H -5.8830 10.8450 11.2020
QMMM: 498 498 H -4.9800 9.6080 12.1450
QMMM: 499 499 H 7.4610 -0.3910 -1.6410
QMMM: 500 500 H 3.2300 -1.2120 -10.1300
QMMM: 501 501 H 4.7110 -1.2460 -10.8380
QMMM: 502 502 H 3.3400 -1.8360 -6.1710
QMMM: 503 503 H 10.4810 -0.6260 -4.6370
QMMM: 504 504 H 10.8910 -2.3410 -4.2810
QMMM: 505 505 H -3.5060 -3.4930 2.2040
QMMM: 506 506 H -5.2610 -3.8310 2.4080
QMMM: 507 507 H -12.3090 0.1820 11.1850
QMMM: 508 508 H -13.0850 -0.3680 9.6590
QMMM: 509 509 H 3.1240 -6.7840 -8.7420
QMMM: 510 510 H 3.7200 -7.5220 -7.2130
QMMM: 511 511 H -8.5650 8.1160 3.3070
QMMM: 512 512 H -8.0620 7.9880 1.5840
QMMM: 513 513 H -3.6730 11.4350 13.2940
QMMM: 514 514 H -4.5560 12.6750 12.3340
QMMM: 515 515 H 12.2010 -1.6070 -2.2500
QMMM: 516 516 H 11.7880 0.1080 -2.6030
QMMM: 517 517 H -4.7030 -5.8200 3.8680
QMMM: 518 518 H -2.9490 -5.4940 3.6380
QMMM: 519 519 H 6.1100 -7.0660 -7.9460
QMMM: 520 520 H 5.4920 -6.4280 -9.5090
QMMM: 521 521 H -12.3740 -2.1830 12.0710
QMMM: 522 522 H -13.1500 -2.7330 10.5440
QMMM: 523 523 H -9.0410 5.6700 1.4640
QMMM: 524 524 H -9.4700 5.7510 3.2090
QMMM: 525 525 H -6.7400 11.8950 13.3390
QMMM: 526 526 H -5.8530 10.6670 14.3090
QMMM: 527 527 H 12.9650 -0.0690 -4.8320
QMMM: 528 528 H 13.3850 -1.7810 -4.4730
QMMM: 529 529 H -3.2130 -5.8240 1.1490
QMMM: 530 530 H -4.9720 -6.1300 1.3740
QMMM: 531 531 H 4.4460 -8.6690 -10.0110
QMMM: 532 532 H 5.0120 -9.2930 -8.4210
QMMM: 533 533 H -14.3270 -0.6400 12.5070
QMMM: 534 534 H -15.1030 -1.1920 10.9810
QMMM: 535 535 H -10.9550 7.7520 2.7390
QMMM: 536 536 H -10.5790 7.6060 0.9860
QMMM: 537 537 H -4.5510 12.5060 15.4480
QMMM: 538 538 H -5.4290 13.7350 14.4710
QMMM: 539 539 H 14.6760 -1.0380 -2.4330
QMMM: 540 540 H 14.2520 0.6740 -2.7880
QMMM: 541 541 H -4.4360 -8.1150 2.8450
QMMM: 542 542 H -2.6790 -7.8170 2.6030
QMMM: 543 543 H 7.4100 -8.8410 -9.1080
QMMM: 544 544 H 6.8330 -8.2810 -10.7170
QMMM: 545 545 H -11.5690 5.2860 0.9640
QMMM: 546 546 H -11.8930 5.4010 2.7290
QMMM: 547 547 H -15.1710 -3.5580 11.8700
QMMM: 548 548 H -14.3950 -3.0060 13.3960
QMMM: 549 549 H -7.6200 12.9680 15.4750
QMMM: 550 550 H -6.7400 11.7430 16.4550
QMMM: 551 551 H 15.4430 0.5070 -5.0110
QMMM: 552 552 H 15.8710 -1.2030 -4.6510
QMMM: 553 553 H -2.9630 -8.1610 0.1170
QMMM: 554 554 H -4.7230 -8.4470 0.3570
QMMM: 555 555 H 5.8250 -10.5560 -11.1450
QMMM: 556 556 H 6.3720 -11.1070 -9.5220
QMMM: 557 557 H -13.3970 7.3960 2.3190
QMMM: 558 558 H -13.1080 7.2400 0.5500
QMMM: 559 559 H 17.1500 -0.4530 -2.6060
QMMM: 560 560 H 16.7190 1.2570 -2.9620
QMMM: 561 561 H -4.1980 -10.4300 1.8350
QMMM: 562 562 H -2.4390 -10.1470 1.5860
QMMM: 563 563 H -16.8920 -3.1900 13.6730
QMMM: 564 564 H -16.3700 -1.4770 13.8510
QMMM: 565 565 H -17.1480 -2.0300 12.3220
QMMM: 566 566 H 8.7740 -10.6600 -10.1850
QMMM: 567 567 H 8.2210 -10.1440 -11.8170
QMMM: 568 568 H -14.1010 4.9200 0.5910
QMMM: 569 569 H -14.3580 5.0570 2.3660
QMMM: 570 570 H -7.2260 13.8050 17.8170
QMMM: 571 571 H -5.4510 13.5960 17.6160
QMMM: 572 572 H -6.3320 14.8230 16.6330
QMMM: 573 573 H 17.9180 1.0960 -5.1810
QMMM: 574 574 H 18.3520 -0.6130 -4.8220
QMMM: 575 575 H -2.7350 -10.4970 -0.8990
QMMM: 576 576 H -4.4950 -10.7750 -0.6500
QMMM: 577 577 H 7.2280 -12.4360 -12.2020
QMMM: 578 578 H 7.7710 -12.9470 -10.5650
QMMM: 579 579 H -15.8730 7.0470 1.9910
QMMM: 580 580 H -15.6350 6.8880 0.2150
QMMM: 581 581 H 19.6280 0.1420 -2.7740
QMMM: 582 582 H 19.1930 1.8500 -3.1320
QMMM: 583 583 H -16.6260 4.5660 0.2900
QMMM: 584 584 H -16.8490 4.7160 2.0690
QMMM: 585 585 H -3.9710 -12.7610 0.8270
QMMM: 586 586 H -2.2120 -12.4830 0.5750
QMMM: 587 587 H 10.1740 -12.5070 -11.2260
QMMM: 588 588 H 9.6290 -12.0090 -12.8660
QMMM: 589 589 H -18.3720 6.7010 1.7100
QMMM: 590 590 H -18.1560 6.5430 -0.0690
QMMM: 591 591 H 21.5110 1.3200 -3.9620
QMMM: 592 592 H 20.4260 1.7020 -5.3460
QMMM: 593 593 H 20.8620 -0.0090 -4.9870
QMMM: 594 594 H -3.0680 -14.2840 -0.9640
QMMM: 595 595 H -2.5070 -12.8640 -1.9170
QMMM: 596 596 H -4.2690 -13.1420 -1.6650
QMMM: 597 597 H 10.4180 -14.4010 -12.8670
QMMM: 598 598 H 8.6610 -14.3260 -13.2460
QMMM: 599 599 H 9.2090 -14.8230 -11.6030
QMMM: 600 600 H -19.1480 4.2190 0.0190
QMMM: 601 601 H -19.3590 4.3750 1.7990
QMMM: 602 602 H -21.5110 4.8790 0.5910
QMMM: 603 603 H -20.9160 6.3470 1.4440
QMMM: 604 604 H -20.7050 6.1920 -0.3390
QMMM: 605 605 H 6.1200 5.6360 -9.9080
QMMM: 606 606 H 3.8980 0.2160 -10.7060
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
iter sqm energy rms gradient
---- ------------------- -----------------------
xmin 10 -4984.5031 kcal/mol 5.9488 kcal/(mol*A)
xmin 20 -5152.2457 kcal/mol 0.9162 kcal/(mol*A)
xmin 30 -5172.6583 kcal/mol 0.5381 kcal/(mol*A)
xmin 40 -5190.7098 kcal/mol 0.4979 kcal/(mol*A)
xmin 50 -5200.5935 kcal/mol 0.7417 kcal/(mol*A)
xmin 60 -5209.6828 kcal/mol 0.5538 kcal/(mol*A)
xmin 70 -5222.4453 kcal/mol 1.7334 kcal/(mol*A)
xmin 80 -5247.8224 kcal/mol 1.2581 kcal/(mol*A)
xmin 90 -5258.2083 kcal/mol 0.3705 kcal/(mol*A)
xmin 100 -5264.2914 kcal/mol 0.2392 kcal/(mol*A)
xmin 110 -5268.1196 kcal/mol 0.1997 kcal/(mol*A)
xmin 120 -5274.8765 kcal/mol 0.6764 kcal/(mol*A)
xmin 130 -5278.4069 kcal/mol 0.2297 kcal/(mol*A)
xmin 140 -5279.8828 kcal/mol 0.1447 kcal/(mol*A)
xmin 150 -5280.6262 kcal/mol 0.1043 kcal/(mol*A)
xmin 160 -5281.3843 kcal/mol 0.1106 kcal/(mol*A)
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\site-packages\chimerax\add_charge\tool.py", line
263, in add_charges
add_nonstandard_res_charges(self.session, residues, charge, method=method)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\add_charge\charge.py", line
319, in add_nonstandard_res_charges
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\add_charge\charge.py", line
602, in nonstd_charge
raise ChargeError(ante_failure_msg)
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL
Check reply log for details
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL
Check reply log for details
File "D:\ChimeraX\bin\lib\site-packages\chimerax\add_charge\charge.py", line
602, in nonstd_charge
raise ChargeError(ante_failure_msg)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 368.39
OpenGL renderer: GeForce GT 730/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: HP
Model: HP EliteDesk 800 G2 SFF
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 34,234,531,840
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-XMAS: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
et-xmlfile: 1.1.0
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openpyxl: 3.1.2
openvr: 1.23.701
packaging: 23.1
pandas: 2.1.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
seaborn: 0.13.0
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → ChargeError during dockprep |
comment:2 by , 23 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
Fix: https://github.com/RBVI/ChimeraX/commit/9d2f163fdd6d0242e544d8ff35067837c71d36f9