| 1 | UCSF ChimeraX version: 1.7.dev202307130149 (2023-07-13)
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| 2 | © 2016-2023 Regents of the University of California. All rights reserved.
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| 3 | How to cite UCSF ChimeraX
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| 4 | open /home/boaz/chimera_models/1qs0.pdb format pdb1qs0.pdb title:
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| 5 | Crystal structure of pseudomonas putida 2-oxoisovalerate dehydrogenase (branched-chain α-keto acid dehydrogenase, E1B) [more info...]
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| 6 |
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| 7 | Chain information for 1qs0.pdb #1
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| 8 | Chain Description UniProt
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| 9 | A 2-oxoisovalerate dehydrogenase α-subunit ODBA_PSEPU 2-408
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| 10 | B 2-oxoisovalerate dehydrogenase β-subunit ODBB_PSEPU 2-339
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| 11 | Non-standard residues in 1qs0.pdb #1
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| 12 | COI â 2-oxo-4-methylpentanoic acid (α-ketoisocaproic acid)
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| 13 | MG â magnesium ion
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| 14 | TPP â thiamine diphosphate
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| 15 | surface include :tpp
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| 16 | coulombic surfaces #1.2Using Amber 20 recommended default charges and atom types for standard residues
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| 17 | Assigning partial charges to residue TPP (net charge -2) with am1-bcc method
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| 18 | Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /tmp/tmprxr5rh03/ante.in.mol2 -fi mol2 -o /tmp/tmprxr5rh03/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n
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| 19 | (TPP)
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| 20 | (TPP) Welcome to antechamber 20.0: molecular input file processor.
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| 21 | (TPP)
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| 22 | (TPP) Info: Finished reading file (/tmp/tmprxr5rh03/ante.in.mol2); atoms read (42), bonds read (43).
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| 23 | (TPP) Info: Determining atomic numbers from atomic symbols which are case sensitive.
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| 24 | (TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
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| 25 | (TPP)
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| 26 | (TPP)
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| 27 | (TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
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| 28 | (TPP) Info: Total number of electrons: 220; net charge: -2
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| 29 | (TPP)
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| 30 | (TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
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| 31 | (TPP) /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/antechamber: Fatal Error!
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| 32 | (TPP) Cannot properly run "/usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out".
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| 33 | Charges failed to converge using fast method; re-running using slower more stable method
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| 34 | Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/antechamber -i /tmp/tmprxr5rh03/ante.in.mol2 -fi mol2 -o /tmp/tmprxr5rh03/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n
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| 35 | (TPP)
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| 36 | (TPP) Welcome to antechamber 20.0: molecular input file processor.
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| 37 | (TPP)
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| 38 | (TPP) Info: Finished reading file (/tmp/tmprxr5rh03/ante.in.mol2); atoms read (42), bonds read (43).
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| 39 | (TPP) Info: Determining atomic numbers from atomic symbols which are case sensitive.
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| 40 | (TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
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| 41 | (TPP)
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| 42 | (TPP)
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| 43 | (TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
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| 44 | (TPP) Info: Total number of electrons: 220; net charge: -2
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| 45 | (TPP)
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| 46 | (TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
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| 47 | (TPP) /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/antechamber: Fatal Error!
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| 48 | (TPP) Cannot properly run "/usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out".
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| 49 |
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| 50 | Contents of sqm.out:
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| 51 | --------------------------------------------------------
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| 52 | AMBER SQM VERSION 19
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| 53 |
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| 54 | By
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| 55 | Ross C. Walker, Michael F. Crowley, Scott Brozell,
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| 56 | Tim Giese, Andreas W. Goetz,
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| 57 | Tai-Sung Lee and David A. Case
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| 58 |
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| 59 | --------------------------------------------------------
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| 60 |
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| 61 |
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| 62 | --------------------------------------------------------------------------------
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| 63 | QM CALCULATION INFO
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| 64 | --------------------------------------------------------------------------------
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| 65 |
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| 66 | | QMMM: Citation for AMBER QMMM Run:
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| 67 | | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
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| 68 |
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| 69 | QMMM: SINGLET STATE CALCULATION
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| 70 | QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 72
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| 71 |
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| 72 | | QMMM: *** Selected Hamiltonian ***
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| 73 | | QMMM: AM1
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| 74 |
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| 75 | | QMMM: *** Parameter sets in use ***
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| 76 | | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
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| 77 | | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
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| 78 | | QMMM: S : M.J.S.DEWAR et al. INORG. CHEM., 29, 3881, (1990)
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| 79 | | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
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| 80 | | QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
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| 81 | | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
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| 82 |
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| 83 | | QMMM: *** SCF convergence criteria ***
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| 84 | | QMMM: Energy change : 0.1D-09 kcal/mol
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| 85 | | QMMM: Error matrix |FP-PF| : 0.1D+00 au
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| 86 | | QMMM: Density matrix change : 0.5D-06
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| 87 | | QMMM: Maximum number of SCF cycles : 1000
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| 88 |
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| 89 | | QMMM: *** Diagonalization Routine Information ***
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| 90 | | QMMM: Pseudo diagonalizations are allowed.
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| 91 | | QMMM: Auto diagonalization routine selection is in use.
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| 92 | | QMMM:
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| 93 | | QMMM: Timing diagonalization routines:
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| 94 | | QMMM: norbs = 120
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| 95 | | QMMM: diag iterations used for timing = 10
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| 96 | | QMMM:
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| 97 | | QMMM: Internal diag routine = 0.046243 seconds
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| 98 | | QMMM: Dspev diag routine = 0.024207 seconds
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| 99 | | QMMM: Dspevd diag routine = 0.017766 seconds
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| 100 | | QMMM: Dspevx diag routine = 0.090484 seconds
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| 101 | | QMMM: Dsyev diag routine = 0.026991 seconds
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| 102 | | QMMM: Dsyevd diag routine = 0.020813 seconds
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| 103 | | QMMM: Dsyevr diag routine = 0.023803 seconds
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| 104 | | QMMM:
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| 105 | | QMMM: Pseudo diag routine = 0.010291 seconds
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| 106 | | QMMM:
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| 107 | | QMMM: Using dspevd routine (diag_routine=3).
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| 108 |
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| 109 | QMMM: QM Region Cartesian Coordinates (*=link atom)
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| 110 | QMMM: QM_NO. MM_NO. ATOM X Y Z
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| 111 | QMMM: 1 1 N -6.5270 -9.5340 108.8420
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| 112 | QMMM: 2 2 C -5.1860 -9.8350 109.0420
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| 113 | QMMM: 3 3 C -4.1430 -8.7560 109.0940
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| 114 | QMMM: 4 4 N -4.7780 -11.0890 109.1960
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| 115 | QMMM: 5 5 C -5.6960 -12.1350 109.1610
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| 116 | QMMM: 6 6 N -5.1880 -13.3540 109.3240
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| 117 | QMMM: 7 7 C -7.1000 -11.8740 108.9590
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| 118 | QMMM: 8 8 C -7.4370 -10.5640 108.8080
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| 119 | QMMM: 9 9 C -8.1400 -12.9880 108.9090
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| 120 | QMMM: 10 10 N -7.9780 -13.7930 107.6090
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| 121 | QMMM: 11 11 C -7.2960 -14.9300 107.6450
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| 122 | QMMM: 12 12 S -7.1510 -15.7280 106.1910
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| 123 | QMMM: 13 13 C -8.0580 -14.4980 105.4120
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| 124 | QMMM: 14 14 C -8.4380 -13.5160 106.3190
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| 125 | QMMM: 15 15 C -9.2300 -12.3130 105.9590
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| 126 | QMMM: 16 16 C -8.3050 -14.6150 103.9530
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| 127 | QMMM: 17 17 C -7.1840 -14.0870 103.0870
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| 128 | QMMM: 18 18 O -7.2870 -14.5610 101.7840
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| 129 | QMMM: 19 19 P -6.2950 -14.6650 100.5520
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| 130 | QMMM: 20 20 O -7.0190 -14.6260 99.2930
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| 131 | QMMM: 21 21 O -5.2170 -13.6750 100.7960
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| 132 | QMMM: 22 22 O -5.6780 -16.0660 100.8100
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| 133 | QMMM: 23 23 P -6.2660 -17.5600 100.7830
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| 134 | QMMM: 24 24 O -7.2020 -17.5030 99.5940
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| 135 | QMMM: 25 25 O -5.0830 -18.4600 100.4010
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| 136 | QMMM: 26 26 O -7.0330 -17.7290 102.0100
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| 137 | QMMM: 27 27 H -8.4780 -10.3200 108.6530
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| 138 | QMMM: 28 28 H -9.1390 -12.5530 108.9430
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| 139 | QMMM: 29 29 H -8.0040 -13.6500 109.7640
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| 140 | QMMM: 30 30 H -6.8630 -15.3130 108.5570
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| 141 | QMMM: 31 31 H -8.4520 -15.6690 103.7150
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| 142 | QMMM: 32 32 H -9.2180 -14.0720 103.7100
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| 143 | QMMM: 33 33 H -6.2300 -14.4070 103.5070
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| 144 | QMMM: 34 34 H -7.2230 -12.9980 103.0760
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| 145 | QMMM: 35 35 H -4.2060 -13.1240 109.3710
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| 146 | QMMM: 36 36 H -5.6510 -14.2500 109.3830
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| 147 | QMMM: 37 37 H -4.0080 -8.3320 108.0990
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| 148 | QMMM: 38 38 H -4.4640 -7.9740 109.7820
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| 149 | QMMM: 39 39 H -3.2000 -9.1790 109.4400
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| 150 | QMMM: 40 40 H -9.3950 -11.7060 106.8490
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| 151 | QMMM: 41 41 H -8.6860 -11.7290 105.2170
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| 152 | QMMM: 42 42 H -10.1910 -12.6210 105.5460
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| 153 |
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| 154 | --------------------------------------------------------------------------------
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| 155 | RESULTS
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| 156 | --------------------------------------------------------------------------------
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| 157 |
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| 158 |
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| 159 | QMMM: ERROR!
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| 160 | QMMM: Unable to achieve self consistency to the tolerances specified
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| 161 | QMMM: No convergence in SCF after 1000 steps.
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| 162 | QMMM: E = -0.8342E+06 DeltaE = -0.8519E-02 DeltaP = 0.2665E-02
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| 163 | QMMM: Smallest DeltaE = 0.8221E-05 DeltaP = 0.1967E-02 Step = 292
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| 164 |
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| 165 |
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| 166 | Failure running ANTECHAMBER for residue TPP
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| 167 | Check reply log for details
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| 168 | select add #15999 atoms, 5942 bonds, 7 pseudobonds, 945 residues, 2 models selected
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| 169 | select subtract #12 models selected
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| 170 | view
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| 171 | help help:user[Repeated 1 time(s)]
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| 172 | help help:user/preferences.html#startup[Repeated 1 time(s)]
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