TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 10000 Info: STEPS PER CYCLE 20 Info: LOAD BALANCE STRATEGY Other Info: LDB PERIOD 4000 steps Info: FIRST LDB TIMESTEP 100 Info: MAX SELF PARTITIONS 50 Info: MAX PAIR PARTITIONS 20 Info: SELF PARTITION ATOMS 125 Info: PAIR PARTITION ATOMS 200 Info: PAIR2 PARTITION ATOMS 400 Info: INITIAL TEMPERATURE 0 Info: CENTER OF MASS MOVING? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: DCD FILENAME new_output/minimize_trajectory.dcd Info: DCD FREQUENCY 100 Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME new_output/minimize Info: RESTART FILENAME new_output/minimize_restart Info: RESTART FREQUENCY 1000 Info: RESTART FILES WILL NOT BE OVERWRITTEN Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 10 Info: SWITCHING OFF 13 Info: PAIRLIST DISTANCE 14.5 Info: MARGIN 0 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 17 Info: ENERGY OUTPUT STEPS 500 Info: TIMING OUTPUT STEPS 500 Info: CONJUGATE GRADIENT MINIMIZATION ACTIVE Info: LINE MINIMIZATION GOAL = 0.0001 Info: BABY STEP SIZE = 0.01 Info: TINY STEP SIZE = 1e-06 Info: USING VERLET I (r-RESPA) MTS SCHEME. Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS Info: RANDOM NUMBER SEED 12345 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB new_input/1i7x_water_pdb.pdb Info: STRUCTURE FILE new_input/1i7x_water_psf.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS parameters/par_all22_prot.inp Warning: DUPLICATE DIHEDRAL ENTRY FOR CP1-C-N-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CP3-N-C-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-C-N-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-C-N-CP3 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-C-NH1-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-CT2-CPH1-CPH1 PREVIOUS VALUES MULTIPLICITY: 1 k=0.2 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.27 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-CT2-CPH1-CPH1 PREVIOUS VALUES MULTIPLICITY: 2 k=0.2 n=1 delta=0 k=0.27 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-NH1-C-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-N-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-N-CP3 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-NH1-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-NH1-CT2 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-NH1-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-NH1-C-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-NH1-C-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-SM-SM-CT2 PREVIOUS VALUES MULTIPLICITY: 1 k=1 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=4.1 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-SM-SM-CT2 PREVIOUS VALUES MULTIPLICITY: 2 k=1 n=1 delta=0 k=4.1 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.9 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-N-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-N-CP3 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-NH1-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-NH1-CT2 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-NH1-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-CT2-CPH1-CPH1 PREVIOUS VALUES MULTIPLICITY: 1 k=0.2 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.27 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-CT2-CPH1-CPH1 PREVIOUS VALUES MULTIPLICITY: 2 k=0.2 n=1 delta=0 k=0.27 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-CT2-S-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=0.24 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.37 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-NH1-C-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-NH1-C-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-S-CT2-CT2 PREVIOUS VALUES MULTIPLICITY: 1 k=0.24 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.37 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-SM-SM-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=1 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=4.1 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-SM-SM-CT3 PREVIOUS VALUES MULTIPLICITY: 2 k=1 n=1 delta=0 k=4.1 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.9 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT1-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.33 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.18 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT1-CT1 PREVIOUS VALUES MULTIPLICITY: 2 k=1.33 n=1 delta=0 k=0.18 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.32 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT1-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=1.33 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.18 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT1-CT3 PREVIOUS VALUES MULTIPLICITY: 2 k=1.33 n=1 delta=0 k=0.18 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.32 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.3 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.3 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT1 PREVIOUS VALUES MULTIPLICITY: 2 k=1.3 n=1 delta=0 k=0.3 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.42 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT2 PREVIOUS VALUES MULTIPLICITY: 1 k=1.3 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.3 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT2 PREVIOUS VALUES MULTIPLICITY: 2 k=1.3 n=1 delta=0 k=0.3 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.42 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=1.3 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.3 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT3 PREVIOUS VALUES MULTIPLICITY: 2 k=1.3 n=1 delta=0 k=0.3 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.42 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR HS-S-CT2-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=0.24 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.15 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR HS-S-CT2-CT1 PREVIOUS VALUES MULTIPLICITY: 2 k=0.24 n=1 delta=0 k=0.15 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.27 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR HS-S-CT2-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=0.24 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.15 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR HS-S-CT2-CT3 PREVIOUS VALUES MULTIPLICITY: 2 k=0.24 n=1 delta=0 k=0.15 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.27 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR N-C-CP1-CP2 PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR N-C-CP1-HB PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR N-C-CP1-N PREVIOUS VALUES MULTIPLICITY: 1 k=0.3 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=-0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR NH1-C-CP1-CP2 PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR NH1-C-CP1-HB PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR NH1-C-CP1-N PREVIOUS VALUES MULTIPLICITY: 1 k=0.3 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=-0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR NH2-CC-CP1-CP2 PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR NH2-CC-CP1-HB PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR NH2-CC-CP1-N PREVIOUS VALUES MULTIPLICITY: 1 k=0.3 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=-0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR O-C-CP1-CP2 PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR O-C-CP1-HB PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR O-C-N-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR O-C-N-CP3 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR O-CC-CP1-CP2 PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR O-CC-CP1-HB PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR OB-CD-OS-CT2 PREVIOUS VALUES MULTIPLICITY: 1 k=0.965 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=3.85 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR OB-CD-OS-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=0.965 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=3.85 n=2 delta=180 Info: SUMMARY OF PARAMETERS: Info: 138 BONDS Info: 341 ANGLES Info: 443 DIHEDRAL Info: 43 IMPROPER Info: 60 VDW Info: 0 VDW_PAIRS Info: **************************** Info: STRUCTURE SUMMARY: Info: 132094 ATOMS Info: 91123 BONDS Info: 57465 ANGLES Info: 23938 DIHEDRALS Info: 1583 IMPROPERS Info: 0 EXCLUSIONS Info: 396279 DEGREES OF FREEDOM Info: 45471 HYDROGEN GROUPS Info: TOTAL MASS = 802586 amu Info: TOTAL CHARGE = -3.99999 e Info: ***************************** Info: Entering startup phase 0 with 32624 kB of memory in use. Info: Entering startup phase 1 with 32624 kB of memory in use. Info: Entering startup phase 2 with 46024 kB of memory in use. Info: Entering startup phase 3 with 46968 kB of memory in use. Info: PATCH GRID IS 7 BY 7 BY 7 Info: REMOVING COM VELOCITY 0 0 0 Info: Entering startup phase 4 with 68040 kB of memory in use. Info: Entering startup phase 5 with 68040 kB of memory in use. Info: Entering startup phase 6 with 68040 kB of memory in use. Info: Entering startup phase 7 with 68040 kB of memory in use. Info: COULOMB TABLE R-SQUARED SPACING: 0.0625 Info: COULOMB TABLE SIZE: 2709 POINTS Info: NONZERO IMPRECISION IN COULOMB TABLE: 1.65436e-24 1.77636e-15 Info: Entering startup phase 8 with 82992 kB of memory in use. Info: Finished startup with 132528 kB of memory in use. Warning: Bad global exclusion count, possible error! Warning: Increasing cutoff during minimization may avoid this. ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP ENERGY: 0 102474.2774 28597.3180 2251.3191 13.0247 -465675.0590 62855.7020 0.0000 0.0000 0.0000 -269483.4178 0.0000 INITIAL STEP: 1e-06 GRADIENT TOLERANCE: 115667 Warning: Bad global exclusion count, possible error! Warning: Increasing cutoff during minimization may avoid this. ENERGY: 1 102187.2354 28579.6222 2251.1781 13.0390 -465693.1838 62039.9575 0.0000 0.0000 0.0000 -270622.1516 0.0000 Warning: Bad global exclusion count, possible error! Warning: Increasing cutoff during minimization may avoid this. ENERGY: 2 101901.2132 28562.0090 2251.0341 13.0543 -465711.3036 61257.7616 0.0000 0.0000 0.0000 -271726.2314 0.0000 Warning: Bad global exclusion count, possible error! Warning: Increasing cutoff during minimization may avoid this. ENERGY: 3 101332.2246 28527.0289 2250.7371 13.0879 -465747.5288 59787.1244 0.0000 0.0000 0.0000 -273837.3259 0.0000 Warning: Bad global exclusion count, possible error! Warning: Increasing cutoff during minimization may avoid this. ENERGY: 4 100206.4463 28458.0384 2250.1056 13.1668 -465819.9220 57178.3435 0.0000 0.0000 0.0000 -277713.8213 0.0000 Warning: Bad global exclusion count, possible error! Warning: Increasing cutoff during minimization may avoid this. ENERGY: 5 98003.4895 28323.7831 2248.6852 13.3695 -465964.4871 53019.0097 0.0000 0.0000 0.0000 -284356.1501 0.0000 Warning: Bad global exclusion count, possible error! Warning: Increasing cutoff during minimization may avoid this. ENERGY: 6 93790.3584 28068.4181 2245.1188 13.9411 -466252.7904 47492.9592 0.0000 0.0000 0.0000 -294641.9948 0.0000 Warning: Bad global exclusion count, possible error! Warning: Increasing cutoff during minimization may avoid this. ENERGY: 7 86119.6387 27587.7151 2232.7169 15.6564 -466826.4783 41937.6106 0.0000 0.0000 0.0000 -308933.1406 0.0000