UCSF ChimeraX version: 1.7.dev202307130149 (2023-07-13) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX open /home/boaz/chimera_models/1qs0.pdb format pdb1qs0.pdb title: Crystal structure of pseudomonas putida 2-oxoisovalerate dehydrogenase (branched-chain α-keto acid dehydrogenase, E1B) [more info...] Chain information for 1qs0.pdb #1 Chain Description UniProt A 2-oxoisovalerate dehydrogenase α-subunit ODBA_PSEPU 2-408 B 2-oxoisovalerate dehydrogenase β-subunit ODBB_PSEPU 2-339 Non-standard residues in 1qs0.pdb #1 COI — 2-oxo-4-methylpentanoic acid (α-ketoisocaproic acid) MG — magnesium ion TPP — thiamine diphosphate surface include :tpp coulombic surfaces #1.2Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue TPP (net charge -2) with am1-bcc method 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 (TPP) (TPP) Welcome to antechamber 20.0: molecular input file processor. (TPP) (TPP) Info: Finished reading file (/tmp/tmprxr5rh03/ante.in.mol2); atoms read (42), bonds read (43). (TPP) Info: Determining atomic numbers from atomic symbols which are case sensitive. (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 (TPP) (TPP) (TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (TPP) Info: Total number of electrons: 220; net charge: -2 (TPP) (TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out (TPP) /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/antechamber: Fatal Error! (TPP) Cannot properly run "/usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out". Charges failed to converge using fast method; re-running using slower more stable method 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 (TPP) (TPP) Welcome to antechamber 20.0: molecular input file processor. (TPP) (TPP) Info: Finished reading file (/tmp/tmprxr5rh03/ante.in.mol2); atoms read (42), bonds read (43). (TPP) Info: Determining atomic numbers from atomic symbols which are case sensitive. (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 (TPP) (TPP) (TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (TPP) Info: Total number of electrons: 220; net charge: -2 (TPP) (TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out (TPP) /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/antechamber: Fatal Error! (TPP) Cannot properly run "/usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out". 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 = 72 | QMMM: *** Selected Hamiltonian *** | QMMM: AM1 | QMMM: *** Parameter sets in use *** | 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: S : M.J.S.DEWAR et al. INORG. CHEM., 29, 3881, (1990) | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989) | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: *** SCF convergence criteria *** | QMMM: Energy change : 0.1D-09 kcal/mol | QMMM: Error matrix |FP-PF| : 0.1D+00 au | QMMM: Density matrix change : 0.5D-06 | 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 = 120 | QMMM: diag iterations used for timing = 10 | QMMM: | QMMM: Internal diag routine = 0.046243 seconds | QMMM: Dspev diag routine = 0.024207 seconds | QMMM: Dspevd diag routine = 0.017766 seconds | QMMM: Dspevx diag routine = 0.090484 seconds | QMMM: Dsyev diag routine = 0.026991 seconds | QMMM: Dsyevd diag routine = 0.020813 seconds | QMMM: Dsyevr diag routine = 0.023803 seconds | QMMM: | QMMM: Pseudo diag routine = 0.010291 seconds | QMMM: | QMMM: Using dspevd routine (diag_routine=3). QMMM: QM Region Cartesian Coordinates (*=link atom) QMMM: QM_NO. MM_NO. ATOM X Y Z QMMM: 1 1 N -6.5270 -9.5340 108.8420 QMMM: 2 2 C -5.1860 -9.8350 109.0420 QMMM: 3 3 C -4.1430 -8.7560 109.0940 QMMM: 4 4 N -4.7780 -11.0890 109.1960 QMMM: 5 5 C -5.6960 -12.1350 109.1610 QMMM: 6 6 N -5.1880 -13.3540 109.3240 QMMM: 7 7 C -7.1000 -11.8740 108.9590 QMMM: 8 8 C -7.4370 -10.5640 108.8080 QMMM: 9 9 C -8.1400 -12.9880 108.9090 QMMM: 10 10 N -7.9780 -13.7930 107.6090 QMMM: 11 11 C -7.2960 -14.9300 107.6450 QMMM: 12 12 S -7.1510 -15.7280 106.1910 QMMM: 13 13 C -8.0580 -14.4980 105.4120 QMMM: 14 14 C -8.4380 -13.5160 106.3190 QMMM: 15 15 C -9.2300 -12.3130 105.9590 QMMM: 16 16 C -8.3050 -14.6150 103.9530 QMMM: 17 17 C -7.1840 -14.0870 103.0870 QMMM: 18 18 O -7.2870 -14.5610 101.7840 QMMM: 19 19 P -6.2950 -14.6650 100.5520 QMMM: 20 20 O -7.0190 -14.6260 99.2930 QMMM: 21 21 O -5.2170 -13.6750 100.7960 QMMM: 22 22 O -5.6780 -16.0660 100.8100 QMMM: 23 23 P -6.2660 -17.5600 100.7830 QMMM: 24 24 O -7.2020 -17.5030 99.5940 QMMM: 25 25 O -5.0830 -18.4600 100.4010 QMMM: 26 26 O -7.0330 -17.7290 102.0100 QMMM: 27 27 H -8.4780 -10.3200 108.6530 QMMM: 28 28 H -9.1390 -12.5530 108.9430 QMMM: 29 29 H -8.0040 -13.6500 109.7640 QMMM: 30 30 H -6.8630 -15.3130 108.5570 QMMM: 31 31 H -8.4520 -15.6690 103.7150 QMMM: 32 32 H -9.2180 -14.0720 103.7100 QMMM: 33 33 H -6.2300 -14.4070 103.5070 QMMM: 34 34 H -7.2230 -12.9980 103.0760 QMMM: 35 35 H -4.2060 -13.1240 109.3710 QMMM: 36 36 H -5.6510 -14.2500 109.3830 QMMM: 37 37 H -4.0080 -8.3320 108.0990 QMMM: 38 38 H -4.4640 -7.9740 109.7820 QMMM: 39 39 H -3.2000 -9.1790 109.4400 QMMM: 40 40 H -9.3950 -11.7060 106.8490 QMMM: 41 41 H -8.6860 -11.7290 105.2170 QMMM: 42 42 H -10.1910 -12.6210 105.5460 -------------------------------------------------------------------------------- RESULTS -------------------------------------------------------------------------------- QMMM: ERROR! QMMM: Unable to achieve self consistency to the tolerances specified QMMM: No convergence in SCF after 1000 steps. QMMM: E = -0.8342E+06 DeltaE = -0.8519E-02 DeltaP = 0.2665E-02 QMMM: Smallest DeltaE = 0.8221E-05 DeltaP = 0.1967E-02 Step = 292 Failure running ANTECHAMBER for residue TPP Check reply log for details select add #15999 atoms, 5942 bonds, 7 pseudobonds, 945 residues, 2 models selected select subtract #12 models selected view help help:user[Repeated 1 time(s)] help help:user/preferences.html#startup[Repeated 1 time(s)]