------------------------------------------------------- Amber 18 PMEMD 2018 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 18 | Run on 06/26/2018 at 19:16:57 | Executable path: pmemd | Working directory: /home/cruzeiro/amber_web/tutorials/advanced/tutorial33/files | Hostname: Unknown [-O]verwriting output File Assignments: | MDIN: min.implicit.mdin | MDOUT: mp8_is.min.mdout | INPCRD: mp8_is.rst7 | PARM: mp8_is.prmtop | RESTRT: mp8_is.min.rst7 | REFC: mp8_is.rst7 | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mp8_is.min.mdinfo | MDFRC: mdfrc Here is the input file: Energy Minimization Stage in Implicit Solvent &cntrl imin=1, ! Perform an energy minimization ntb=0, ! Boundaries (=0, non-periodic) cut=1000.0, ! Cutoff ntmin=1, ! Method of minimization ncyc=100, ! Number of steepest descent cycles maxcyc=4000, ! Maximum number of minimization cycles igb=2, ! GB model saltcon=0.1, ! Salt concentration ntr=1, ! Turn on positional restraints restraintmask='@CA,C,O,N|(:HEH,PRN)@FE,NA,NB,NC,ND,C3D,C2A,C3B,C2C,CA,CB', restraint_wt=10.0, ! 10 kcal/mol.A**2 restraint force constant / Note: ig = -1. Setting random seed to 168404 based on wallclock time in microseconds. | irandom = 1, using AMBER's internal random number generator (default). | Conditional Compilation Defines Used: | PUBFFT | BINTRAJ | EMIL | New format PARM file being parsed. | Version = 1.000 Date = 06/19/18 Time = 19:53:04 | Note: 1-4 EEL scale factors are being read from the topology file. | Note: 1-4 VDW scale factors are being read from the topology file. | INFO: Reading atomic numbers from topology file. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- NATOM = 237 NTYPES = 13 NBONH = 115 MBONA = 133 NTHETH = 247 MTHETA = 206 NPHIH = 450 MPHIA = 440 NHPARM = 0 NPARM = 0 NNB = 1352 NRES = 16 NBONA = 133 NTHETA = 206 NPHIA = 440 NUMBND = 35 NUMANG = 83 NPTRA = 37 NATYP = 23 NPHB = 0 IFBOX = 0 NMXRS = 87 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are H(N)-modified Bondi radii (mbondi2) -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 2, ntpr = 50, ntrx = 1, ntwr = 1 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 2, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut =1000.00000, intdiel = 1.00000 saltcon = 0.10000, offset = 0.09000, gbalpha= 0.80000 gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 1 restraint_wt = 10.00000 Energy minimization: maxcyc = 4000, ncyc = 100, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 1 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES default_name Mask @CA,C,O,N|(:HEH,PRN)@FE,NA,NB,NC,ND,C3D,C2A,C3B,C2C,CA,CB; matches 127 atoms -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- default_name begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 | Dynamic Memory, Types Used: | Reals 7915 | Integers 24523 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP ENERGY RMS GMAX NAME NUMBER 1 9.0374E+03 2.6201E+03 3.2978E+04 O 24 BOND = 151.7693 ANGLE = 646.3001 DIHED = 111.5636 VDWAALS = 4553.0822 EEL = -710.5857 EGB = -313.1620 1-4 VDW = 4014.5901 1-4 EEL = 583.8746 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -1.6354E+02 3.3026E+00 2.0369E+01 H 26 BOND = 14.2017 ANGLE = 109.2518 DIHED = 108.3513 VDWAALS = -37.0221 EEL = -693.3720 EGB = -328.4681 1-4 VDW = 37.8970 1-4 EEL = 569.9742 RESTRAINT = 55.6489 EAMBER = -219.1862 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.9606E+02 2.2641E+00 1.8055E+01 CD22 210 BOND = 12.7298 ANGLE = 91.7959 DIHED = 102.4306 VDWAALS = -45.3782 EEL = -687.4447 EGB = -331.8712 1-4 VDW = 33.7978 1-4 EEL = 565.8599 RESTRAINT = 62.0204 EAMBER = -258.0801 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -2.2827E+02 1.1818E+00 6.1747E+00 O 24 BOND = 11.8635 ANGLE = 83.3968 DIHED = 93.9243 VDWAALS = -55.0750 EEL = -681.0178 EGB = -339.6002 1-4 VDW = 32.4565 1-4 EEL = 563.8358 RESTRAINT = 61.9444 EAMBER = -290.2163 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -2.3258E+02 7.8514E-01 5.0724E+00 CA 27 BOND = 11.7946 ANGLE = 82.5990 DIHED = 91.9546 VDWAALS = -55.2266 EEL = -679.8071 EGB = -340.8013 1-4 VDW = 32.1363 1-4 EEL = 563.4107 RESTRAINT = 61.3613 EAMBER = -293.9398 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -2.3577E+02 7.9730E-01 5.3645E+00 CA 27 BOND = 11.8292 ANGLE = 82.0726 DIHED = 90.7466 VDWAALS = -55.4034 EEL = -678.6175 EGB = -342.0450 1-4 VDW = 31.8220 1-4 EEL = 563.1285 RESTRAINT = 60.6943 EAMBER = -296.4670 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -2.3831E+02 7.2972E-01 4.7923E+00 CA 27 BOND = 11.8282 ANGLE = 81.6929 DIHED = 89.9483 VDWAALS = -55.4967 EEL = -677.5062 EGB = -343.2978 1-4 VDW = 31.4990 1-4 EEL = 562.9800 RESTRAINT = 60.0450 EAMBER = -298.3522 NSTEP ENERGY RMS GMAX NAME NUMBER 350 -2.4029E+02 6.3352E-01 3.8206E+00 O2 233 BOND = 11.7933 ANGLE = 81.4311 DIHED = 89.4768 VDWAALS = -55.5671 EEL = -676.6397 EGB = -344.4618 1-4 VDW = 31.1965 1-4 EEL = 563.0013 RESTRAINT = 59.4818 EAMBER = -299.7696 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -2.4192E+02 5.4060E-01 2.8237E+00 N 25 BOND = 11.7445 ANGLE = 81.2414 DIHED = 89.2574 VDWAALS = -55.6531 EEL = -676.1098 EGB = -345.4144 1-4 VDW = 30.9287 1-4 EEL = 563.1460 RESTRAINT = 58.9379 EAMBER = -300.8593 NSTEP ENERGY RMS GMAX NAME NUMBER 450 -2.4374E+02 8.3301E-01 5.2797E+00 O 12 BOND = 12.1104 ANGLE = 81.1207 DIHED = 89.1768 VDWAALS = -55.6119 EEL = -675.5117 EGB = -346.9246 1-4 VDW = 30.4312 1-4 EEL = 563.3193 RESTRAINT = 58.1508 EAMBER = -301.8897 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -2.4523E+02 5.6261E-01 2.5732E+00 CB2 201 BOND = 11.8259 ANGLE = 80.9133 DIHED = 89.3239 VDWAALS = -55.9635 EEL = -676.0405 EGB = -347.3348 1-4 VDW = 30.2675 1-4 EEL = 563.9178 RESTRAINT = 57.8602 EAMBER = -303.0903 NSTEP ENERGY RMS GMAX NAME NUMBER 550 -2.4644E+02 9.6510E-01 4.9517E+00 CB2 201 BOND = 11.9355 ANGLE = 80.7549 DIHED = 89.3766 VDWAALS = -55.9444 EEL = -676.8862 EGB = -347.6834 1-4 VDW = 30.1475 1-4 EEL = 564.7911 RESTRAINT = 57.0640 EAMBER = -303.5084 NSTEP ENERGY RMS GMAX NAME NUMBER 600 -2.4728E+02 3.7048E-01 1.7099E+00 O 12 BOND = 11.7737 ANGLE = 80.5269 DIHED = 89.5744 VDWAALS = -55.9338 EEL = -677.2427 EGB = -347.7544 1-4 VDW = 30.0754 1-4 EEL = 565.0565 RESTRAINT = 56.6401 EAMBER = -303.9240 NSTEP ENERGY RMS GMAX NAME NUMBER 650 -2.4782E+02 5.7130E-01 3.3287E+00 OE2 112 BOND = 11.8190 ANGLE = 80.4496 DIHED = 89.6557 VDWAALS = -55.8986 EEL = -677.8328 EGB = -347.5059 1-4 VDW = 30.1245 1-4 EEL = 565.0897 RESTRAINT = 56.2775 EAMBER = -304.0987 NSTEP ENERGY RMS GMAX NAME NUMBER 700 -2.4808E+02 2.0755E-01 1.1366E+00 CB2 201 BOND = 11.6497 ANGLE = 80.3478 DIHED = 89.6440 VDWAALS = -55.8293 EEL = -677.8885 EGB = -347.4547 1-4 VDW = 30.1637 1-4 EEL = 565.0521 RESTRAINT = 56.2322 EAMBER = -304.3152 NSTEP ENERGY RMS GMAX NAME NUMBER 750 -2.4823E+02 3.8406E-01 2.2421E+00 CA 9 BOND = 11.6653 ANGLE = 80.3143 DIHED = 89.6981 VDWAALS = -55.7868 EEL = -677.9872 EGB = -347.4575 1-4 VDW = 30.1227 1-4 EEL = 565.0081 RESTRAINT = 56.1892 EAMBER = -304.4230 NSTEP ENERGY RMS GMAX NAME NUMBER 800 -2.4837E+02 3.0762E-01 1.8181E+00 CH3 15 BOND = 11.5476 ANGLE = 80.3912 DIHED = 89.7539 VDWAALS = -55.7373 EEL = -678.0805 EGB = -347.4079 1-4 VDW = 30.0966 1-4 EEL = 564.9474 RESTRAINT = 56.1173 EAMBER = -304.4888 NSTEP ENERGY RMS GMAX NAME NUMBER 850 -2.4850E+02 1.4234E-01 8.9066E-01 CB2 201 BOND = 11.5489 ANGLE = 80.3512 DIHED = 89.8260 VDWAALS = -55.7694 EEL = -678.1449 EGB = -347.3872 1-4 VDW = 30.0630 1-4 EEL = 564.9395 RESTRAINT = 56.0744 EAMBER = -304.5729 NSTEP ENERGY RMS GMAX NAME NUMBER 900 -2.4881E+02 8.9474E-02 5.3324E-01 OE2 112 BOND = 11.5192 ANGLE = 80.2486 DIHED = 89.9485 VDWAALS = -55.7203 EEL = -678.3303 EGB = -347.2805 1-4 VDW = 30.0245 1-4 EEL = 564.8023 RESTRAINT = 55.9827 EAMBER = -304.7880 NSTEP ENERGY RMS GMAX NAME NUMBER 950 -2.4896E+02 1.0092E-01 5.3707E-01 CB 104 BOND = 11.4952 ANGLE = 80.2631 DIHED = 90.0311 VDWAALS = -55.7251 EEL = -678.3319 EGB = -347.3183 1-4 VDW = 29.9869 1-4 EEL = 564.7378 RESTRAINT = 55.9027 EAMBER = -304.8613 NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -2.4912E+02 9.9895E-02 5.8092E-01 CA 9 BOND = 11.5195 ANGLE = 80.2296 DIHED = 90.1105 VDWAALS = -55.7380 EEL = -678.2917 EGB = -347.3599 1-4 VDW = 29.9371 1-4 EEL = 564.6355 RESTRAINT = 55.8356 EAMBER = -304.9573 NSTEP ENERGY RMS GMAX NAME NUMBER 1050 -2.4928E+02 1.4451E-01 6.7975E-01 C 56 BOND = 11.5338 ANGLE = 80.1546 DIHED = 90.1851 VDWAALS = -55.7513 EEL = -678.2321 EGB = -347.4014 1-4 VDW = 29.8986 1-4 EEL = 564.5306 RESTRAINT = 55.8043 EAMBER = -305.0820 NSTEP ENERGY RMS GMAX NAME NUMBER 1100 -2.4953E+02 1.0761E-01 7.0654E-01 CA 9 BOND = 11.4875 ANGLE = 80.1181 DIHED = 90.2675 VDWAALS = -55.7694 EEL = -678.1618 EGB = -347.4524 1-4 VDW = 29.8525 1-4 EEL = 564.3790 RESTRAINT = 55.7442 EAMBER = -305.2790 NSTEP ENERGY RMS GMAX NAME NUMBER 1150 -2.4985E+02 1.3519E-01 6.9176E-01 O 12 BOND = 11.4896 ANGLE = 79.9971 DIHED = 90.3391 VDWAALS = -55.7830 EEL = -678.0734 EGB = -347.5215 1-4 VDW = 29.8054 1-4 EEL = 564.2089 RESTRAINT = 55.6877 EAMBER = -305.5378 NSTEP ENERGY RMS GMAX NAME NUMBER 1200 -2.5018E+02 1.8620E-01 1.2494E+00 OE1 111 BOND = 11.5869 ANGLE = 79.7460 DIHED = 90.3745 VDWAALS = -55.8153 EEL = -677.9837 EGB = -347.5535 1-4 VDW = 29.7590 1-4 EEL = 564.0620 RESTRAINT = 55.6478 EAMBER = -305.8240 NSTEP ENERGY RMS GMAX NAME NUMBER 1250 -2.5055E+02 1.1906E-01 5.6171E-01 HE21 54 BOND = 11.5528 ANGLE = 79.5990 DIHED = 90.3929 VDWAALS = -55.8733 EEL = -677.9829 EGB = -347.5325 1-4 VDW = 29.7365 1-4 EEL = 563.9228 RESTRAINT = 55.6345 EAMBER = -306.1847 NSTEP ENERGY RMS GMAX NAME NUMBER 1300 -2.5107E+02 1.6451E-01 8.0754E-01 C 68 BOND = 11.4979 ANGLE = 79.4161 DIHED = 90.3435 VDWAALS = -55.9572 EEL = -678.1169 EGB = -347.4203 1-4 VDW = 29.7258 1-4 EEL = 563.8184 RESTRAINT = 55.6184 EAMBER = -306.6927 NSTEP ENERGY RMS GMAX NAME NUMBER 1350 -2.5169E+02 1.0549E-01 5.1878E-01 CH3 2 BOND = 11.4822 ANGLE = 79.0951 DIHED = 90.1876 VDWAALS = -56.0112 EEL = -678.4132 EGB = -347.1489 1-4 VDW = 29.7386 1-4 EEL = 563.7871 RESTRAINT = 55.5881 EAMBER = -307.2827 NSTEP ENERGY RMS GMAX NAME NUMBER 1400 -2.5225E+02 1.8674E-01 1.3192E+00 OE1 111 BOND = 11.5139 ANGLE = 78.8767 DIHED = 89.9338 VDWAALS = -56.1073 EEL = -678.8400 EGB = -346.7440 1-4 VDW = 29.7659 1-4 EEL = 563.7710 RESTRAINT = 55.5774 EAMBER = -307.8300 NSTEP ENERGY RMS GMAX NAME NUMBER 1450 -2.5261E+02 1.2266E-01 9.1067E-01 HH33 18 BOND = 11.4767 ANGLE = 78.7464 DIHED = 89.7659 VDWAALS = -56.1335 EEL = -679.1764 EGB = -346.4706 1-4 VDW = 29.7923 1-4 EEL = 563.8201 RESTRAINT = 55.5707 EAMBER = -308.1792 NSTEP ENERGY RMS GMAX NAME NUMBER 1500 -2.5297E+02 1.4094E-01 7.5517E-01 OE1 111 BOND = 11.4684 ANGLE = 78.5458 DIHED = 89.5932 VDWAALS = -56.1910 EEL = -679.6220 EGB = -346.0743 1-4 VDW = 29.8380 1-4 EEL = 563.9265 RESTRAINT = 55.5429 EAMBER = -308.5156 NSTEP ENERGY RMS GMAX NAME NUMBER 1550 -2.5321E+02 1.9533E-01 1.1734E+00 H 14 BOND = 11.5363 ANGLE = 78.4210 DIHED = 89.5163 VDWAALS = -56.2497 EEL = -679.8478 EGB = -345.8843 1-4 VDW = 29.8537 1-4 EEL = 563.9309 RESTRAINT = 55.5130 EAMBER = -308.7237 NSTEP ENERGY RMS GMAX NAME NUMBER 1600 -2.5342E+02 1.8750E-01 1.2166E+00 HH33 18 BOND = 11.5217 ANGLE = 78.2949 DIHED = 89.4799 VDWAALS = -56.2661 EEL = -680.1442 EGB = -345.6256 1-4 VDW = 29.8761 1-4 EEL = 563.9718 RESTRAINT = 55.4719 EAMBER = -308.8916 NSTEP ENERGY RMS GMAX NAME NUMBER 1650 -2.5360E+02 1.0169E-01 5.8923E-01 HH31 16 BOND = 11.4752 ANGLE = 78.2168 DIHED = 89.4854 VDWAALS = -56.3798 EEL = -680.3513 EGB = -345.4531 1-4 VDW = 29.9083 1-4 EEL = 564.0293 RESTRAINT = 55.4741 EAMBER = -309.0692 NSTEP ENERGY RMS GMAX NAME NUMBER 1700 -2.5374E+02 8.6098E-02 3.3829E-01 H 65 BOND = 11.4762 ANGLE = 78.1321 DIHED = 89.4892 VDWAALS = -56.4330 EEL = -680.5192 EGB = -345.2944 1-4 VDW = 29.9283 1-4 EEL = 564.0217 RESTRAINT = 55.4611 EAMBER = -309.1991 NSTEP ENERGY RMS GMAX NAME NUMBER 1750 -2.5389E+02 9.5782E-02 5.0131E-01 N 13 BOND = 11.5069 ANGLE = 78.0071 DIHED = 89.4880 VDWAALS = -56.4877 EEL = -680.7084 EGB = -345.1117 1-4 VDW = 29.9562 1-4 EEL = 564.0087 RESTRAINT = 55.4518 EAMBER = -309.3409 NSTEP ENERGY RMS GMAX NAME NUMBER 1800 -2.5403E+02 1.3729E-01 6.4532E-01 C 11 BOND = 11.4724 ANGLE = 77.9427 DIHED = 89.4884 VDWAALS = -56.5377 EEL = -680.9080 EGB = -344.9331 1-4 VDW = 29.9781 1-4 EEL = 564.0227 RESTRAINT = 55.4434 EAMBER = -309.4745 NSTEP ENERGY RMS GMAX NAME NUMBER 1850 -2.5416E+02 2.0292E-01 1.1095E+00 CE12 207 BOND = 11.4710 ANGLE = 77.8401 DIHED = 89.4800 VDWAALS = -56.5911 EEL = -681.1111 EGB = -344.7310 1-4 VDW = 30.0050 1-4 EEL = 564.0358 RESTRAINT = 55.4443 EAMBER = -309.6014 NSTEP ENERGY RMS GMAX NAME NUMBER 1900 -2.5428E+02 1.4790E-01 1.1261E+00 CA 9 BOND = 11.4916 ANGLE = 77.7710 DIHED = 89.4695 VDWAALS = -56.6333 EEL = -681.2951 EGB = -344.5698 1-4 VDW = 30.0238 1-4 EEL = 564.0246 RESTRAINT = 55.4416 EAMBER = -309.7177 NSTEP ENERGY RMS GMAX NAME NUMBER 1950 -2.5439E+02 1.0115E-01 5.0401E-01 N 13 BOND = 11.4561 ANGLE = 77.7502 DIHED = 89.4664 VDWAALS = -56.6895 EEL = -681.5287 EGB = -344.3583 1-4 VDW = 30.0505 1-4 EEL = 564.0279 RESTRAINT = 55.4357 EAMBER = -309.8254 NSTEP ENERGY RMS GMAX NAME NUMBER 2000 -2.5449E+02 1.1828E-01 5.4621E-01 C 11 BOND = 11.4538 ANGLE = 77.7185 DIHED = 89.4492 VDWAALS = -56.7154 EEL = -681.7002 EGB = -344.2057 1-4 VDW = 30.0577 1-4 EEL = 564.0243 RESTRAINT = 55.4283 EAMBER = -309.9179 NSTEP ENERGY RMS GMAX NAME NUMBER 2050 -2.5458E+02 9.6741E-02 3.1809E-01 C 98 BOND = 11.4592 ANGLE = 77.6737 DIHED = 89.4245 VDWAALS = -56.7419 EEL = -681.8795 EGB = -344.0230 1-4 VDW = 30.0690 1-4 EEL = 564.0046 RESTRAINT = 55.4285 EAMBER = -310.0135 NSTEP ENERGY RMS GMAX NAME NUMBER 2100 -2.5467E+02 8.3737E-02 4.2424E-01 OE1 111 BOND = 11.4418 ANGLE = 77.6307 DIHED = 89.4148 VDWAALS = -56.7757 EEL = -682.0855 EGB = -343.8443 1-4 VDW = 30.0867 1-4 EEL = 564.0338 RESTRAINT = 55.4242 EAMBER = -310.0977 NSTEP ENERGY RMS GMAX NAME NUMBER 2150 -2.5475E+02 1.9476E-01 1.0770E+00 OE2 112 BOND = 11.4353 ANGLE = 77.5837 DIHED = 89.3944 VDWAALS = -56.7942 EEL = -682.2877 EGB = -343.6305 1-4 VDW = 30.0981 1-4 EEL = 564.0214 RESTRAINT = 55.4264 EAMBER = -310.1795 NSTEP ENERGY RMS GMAX NAME NUMBER 2200 -2.5483E+02 1.5780E-01 9.0876E-01 OE1 111 BOND = 11.4276 ANGLE = 77.5610 DIHED = 89.3690 VDWAALS = -56.8183 EEL = -682.5253 EGB = -343.4395 1-4 VDW = 30.1177 1-4 EEL = 564.0512 RESTRAINT = 55.4248 EAMBER = -310.2566 NSTEP ENERGY RMS GMAX NAME NUMBER 2250 -2.5491E+02 1.5630E-01 6.8654E-01 CBC1 182 BOND = 11.4512 ANGLE = 77.5708 DIHED = 89.3393 VDWAALS = -56.8365 EEL = -682.8505 EGB = -343.2110 1-4 VDW = 30.1270 1-4 EEL = 564.0801 RESTRAINT = 55.4220 EAMBER = -310.3296 NSTEP ENERGY RMS GMAX NAME NUMBER 2300 -2.5498E+02 1.2958E-01 7.8516E-01 CE12 207 BOND = 11.4505 ANGLE = 77.5482 DIHED = 89.3084 VDWAALS = -56.8238 EEL = -683.1610 EGB = -342.9766 1-4 VDW = 30.1453 1-4 EEL = 564.1203 RESTRAINT = 55.4097 EAMBER = -310.3888 NSTEP ENERGY RMS GMAX NAME NUMBER 2350 -2.5505E+02 2.0209E-01 1.7637E+00 CD22 210 BOND = 11.4829 ANGLE = 77.5330 DIHED = 89.2631 VDWAALS = -56.8198 EEL = -683.6051 EGB = -342.6712 1-4 VDW = 30.1634 1-4 EEL = 564.1920 RESTRAINT = 55.4093 EAMBER = -310.4617 NSTEP ENERGY RMS GMAX NAME NUMBER 2400 -2.5513E+02 1.1240E-01 8.3639E-01 C 5 BOND = 11.4296 ANGLE = 77.5626 DIHED = 89.2238 VDWAALS = -56.7946 EEL = -684.0056 EGB = -342.3957 1-4 VDW = 30.1932 1-4 EEL = 564.2492 RESTRAINT = 55.4085 EAMBER = -310.5376 NSTEP ENERGY RMS GMAX NAME NUMBER 2450 -2.5520E+02 1.3982E-01 8.3685E-01 CD22 210 BOND = 11.4539 ANGLE = 77.5647 DIHED = 89.1780 VDWAALS = -56.7701 EEL = -684.4184 EGB = -342.1337 1-4 VDW = 30.2103 1-4 EEL = 564.3136 RESTRAINT = 55.4039 EAMBER = -310.6019 NSTEP ENERGY RMS GMAX NAME NUMBER 2500 -2.5526E+02 7.2796E-02 3.9111E-01 CE12 207 BOND = 11.4437 ANGLE = 77.5738 DIHED = 89.1445 VDWAALS = -56.7458 EEL = -684.8132 EGB = -341.8751 1-4 VDW = 30.2273 1-4 EEL = 564.3811 RESTRAINT = 55.4006 EAMBER = -310.6636 NSTEP ENERGY RMS GMAX NAME NUMBER 2550 -2.5533E+02 1.2276E-01 5.8267E-01 O1 232 BOND = 11.4517 ANGLE = 77.5923 DIHED = 89.0934 VDWAALS = -56.7110 EEL = -685.2846 EGB = -341.5859 1-4 VDW = 30.2443 1-4 EEL = 564.4532 RESTRAINT = 55.4118 EAMBER = -310.7467 NSTEP ENERGY RMS GMAX NAME NUMBER 2600 -2.5540E+02 1.8166E-01 1.5903E+00 O1 219 BOND = 11.4636 ANGLE = 77.5994 DIHED = 89.0387 VDWAALS = -56.6712 EEL = -685.7269 EGB = -341.2942 1-4 VDW = 30.2636 1-4 EEL = 564.5060 RESTRAINT = 55.4168 EAMBER = -310.8209 NSTEP ENERGY RMS GMAX NAME NUMBER 2650 -2.5548E+02 1.2735E-01 8.0098E-01 C 11 BOND = 11.4326 ANGLE = 77.6462 DIHED = 88.9787 VDWAALS = -56.6277 EEL = -686.1450 EGB = -341.0357 1-4 VDW = 30.2856 1-4 EEL = 564.5539 RESTRAINT = 55.4332 EAMBER = -310.9114 NSTEP ENERGY RMS GMAX NAME NUMBER 2700 -2.5554E+02 1.0912E-01 7.0778E-01 CE12 207 BOND = 11.4594 ANGLE = 77.6424 DIHED = 88.9439 VDWAALS = -56.6115 EEL = -686.4966 EGB = -340.8201 1-4 VDW = 30.3013 1-4 EEL = 564.6215 RESTRAINT = 55.4169 EAMBER = -310.9597 NSTEP ENERGY RMS GMAX NAME NUMBER 2750 -2.5560E+02 8.6556E-02 4.9284E-01 O1 232 BOND = 11.4636 ANGLE = 77.6398 DIHED = 88.9026 VDWAALS = -56.5798 EEL = -686.7823 EGB = -340.6360 1-4 VDW = 30.3073 1-4 EEL = 564.6590 RESTRAINT = 55.4280 EAMBER = -311.0257 NSTEP ENERGY RMS GMAX NAME NUMBER 2800 -2.5565E+02 1.7564E-01 1.0864E+00 O1 232 BOND = 11.4931 ANGLE = 77.6160 DIHED = 88.8692 VDWAALS = -56.5559 EEL = -687.0625 EGB = -340.4331 1-4 VDW = 30.3129 1-4 EEL = 564.6768 RESTRAINT = 55.4371 EAMBER = -311.0834 NSTEP ENERGY RMS GMAX NAME NUMBER 2850 -2.5569E+02 1.0780E-01 7.4972E-01 OE2 112 BOND = 11.4519 ANGLE = 77.6458 DIHED = 88.8459 VDWAALS = -56.5421 EEL = -687.2521 EGB = -340.2975 1-4 VDW = 30.3253 1-4 EEL = 564.7021 RESTRAINT = 55.4268 EAMBER = -311.1208 NSTEP ENERGY RMS GMAX NAME NUMBER 2900 -2.5574E+02 7.9537E-02 4.2507E-01 HB 75 BOND = 11.4515 ANGLE = 77.6554 DIHED = 88.8219 VDWAALS = -56.5314 EEL = -687.4517 EGB = -340.1651 1-4 VDW = 30.3315 1-4 EEL = 564.7282 RESTRAINT = 55.4243 EAMBER = -311.1597 NSTEP ENERGY RMS GMAX NAME NUMBER 2950 -2.5577E+02 7.2241E-02 3.0770E-01 HB 75 BOND = 11.4546 ANGLE = 77.6449 DIHED = 88.7994 VDWAALS = -56.5222 EEL = -687.6178 EGB = -340.0401 1-4 VDW = 30.3362 1-4 EEL = 564.7459 RESTRAINT = 55.4268 EAMBER = -311.1991 NSTEP ENERGY RMS GMAX NAME NUMBER 3000 -2.5580E+02 6.3431E-02 3.7186E-01 OE1 111 BOND = 11.4480 ANGLE = 77.6410 DIHED = 88.7781 VDWAALS = -56.5159 EEL = -687.7451 EGB = -339.9394 1-4 VDW = 30.3425 1-4 EEL = 564.7571 RESTRAINT = 55.4309 EAMBER = -311.2337 NSTEP ENERGY RMS GMAX NAME NUMBER 3050 -2.5585E+02 1.4765E-01 6.4998E-01 C2D 173 BOND = 11.4347 ANGLE = 77.6521 DIHED = 88.7368 VDWAALS = -56.5268 EEL = -687.9426 EGB = -339.7832 1-4 VDW = 30.3378 1-4 EEL = 564.8008 RESTRAINT = 55.4445 EAMBER = -311.2905 NSTEP ENERGY RMS GMAX NAME NUMBER 3100 -2.5587E+02 7.4302E-02 3.5712E-01 OE1 111 BOND = 11.4228 ANGLE = 77.6472 DIHED = 88.7267 VDWAALS = -56.5243 EEL = -688.0465 EGB = -339.6995 1-4 VDW = 30.3442 1-4 EEL = 564.8182 RESTRAINT = 55.4401 EAMBER = -311.3112 NSTEP ENERGY RMS GMAX NAME NUMBER 3150 -2.5589E+02 4.3735E-02 2.0422E-01 OE1 111 BOND = 11.4225 ANGLE = 77.6475 DIHED = 88.7105 VDWAALS = -56.5228 EEL = -688.1325 EGB = -339.6206 1-4 VDW = 30.3463 1-4 EEL = 564.8183 RESTRAINT = 55.4383 EAMBER = -311.3308 NSTEP ENERGY RMS GMAX NAME NUMBER 3200 -2.5591E+02 3.3666E-02 1.6406E-01 CG 107 BOND = 11.4251 ANGLE = 77.6300 DIHED = 88.7006 VDWAALS = -56.5140 EEL = -688.2204 EGB = -339.5488 1-4 VDW = 30.3516 1-4 EEL = 564.8302 RESTRAINT = 55.4338 EAMBER = -311.3458 NSTEP ENERGY RMS GMAX NAME NUMBER 3250 -2.5593E+02 6.5199E-02 5.6926E-01 OE2 112 BOND = 11.4302 ANGLE = 77.6227 DIHED = 88.6904 VDWAALS = -56.5198 EEL = -688.2986 EGB = -339.4806 1-4 VDW = 30.3496 1-4 EEL = 564.8378 RESTRAINT = 55.4385 EAMBER = -311.3683 NSTEP ENERGY RMS GMAX NAME NUMBER 3300 -2.5595E+02 7.0342E-02 4.4453E-01 C 56 BOND = 11.4258 ANGLE = 77.6254 DIHED = 88.6769 VDWAALS = -56.5211 EEL = -688.3814 EGB = -339.4113 1-4 VDW = 30.3508 1-4 EEL = 564.8447 RESTRAINT = 55.4427 EAMBER = -311.3901 NSTEP ENERGY RMS GMAX NAME NUMBER 3350 -2.5596E+02 4.2466E-02 2.6315E-01 O 12 BOND = 11.4168 ANGLE = 77.6229 DIHED = 88.6625 VDWAALS = -56.5151 EEL = -688.4520 EGB = -339.3411 1-4 VDW = 30.3557 1-4 EEL = 564.8452 RESTRAINT = 55.4407 EAMBER = -311.4052 NSTEP ENERGY RMS GMAX NAME NUMBER 3400 -2.5598E+02 9.1588E-02 5.3895E-01 CG 231 BOND = 11.4190 ANGLE = 77.6091 DIHED = 88.6492 VDWAALS = -56.5176 EEL = -688.5290 EGB = -339.2699 1-4 VDW = 30.3543 1-4 EEL = 564.8559 RESTRAINT = 55.4492 EAMBER = -311.4290 NSTEP ENERGY RMS GMAX NAME NUMBER 3450 -2.5600E+02 7.2337E-02 2.9119E-01 O 12 BOND = 11.4156 ANGLE = 77.6194 DIHED = 88.6292 VDWAALS = -56.5278 EEL = -688.6208 EGB = -339.1827 1-4 VDW = 30.3538 1-4 EEL = 564.8608 RESTRAINT = 55.4531 EAMBER = -311.4526 NSTEP ENERGY RMS GMAX NAME NUMBER 3500 -2.5601E+02 3.0207E-02 1.4153E-01 C 11 BOND = 11.4208 ANGLE = 77.6154 DIHED = 88.6251 VDWAALS = -56.5247 EEL = -688.6848 EGB = -339.1256 1-4 VDW = 30.3574 1-4 EEL = 564.8651 RESTRAINT = 55.4377 EAMBER = -311.4513 NSTEP ENERGY RMS GMAX NAME NUMBER 3550 -2.5602E+02 3.8973E-02 1.8231E-01 O1 232 BOND = 11.4211 ANGLE = 77.6140 DIHED = 88.6156 VDWAALS = -56.5259 EEL = -688.7352 EGB = -339.0834 1-4 VDW = 30.3575 1-4 EEL = 564.8701 RESTRAINT = 55.4428 EAMBER = -311.4663 NSTEP ENERGY RMS GMAX NAME NUMBER 3600 -2.5603E+02 6.0820E-02 4.5685E-01 CG 231 BOND = 11.4164 ANGLE = 77.6132 DIHED = 88.6070 VDWAALS = -56.5275 EEL = -688.7855 EGB = -339.0370 1-4 VDW = 30.3589 1-4 EEL = 564.8745 RESTRAINT = 55.4471 EAMBER = -311.4801 NSTEP ENERGY RMS GMAX NAME NUMBER 3650 -2.5605E+02 6.9377E-02 3.5326E-01 CG 107 BOND = 11.4187 ANGLE = 77.6019 DIHED = 88.5892 VDWAALS = -56.5340 EEL = -688.8707 EGB = -338.9543 1-4 VDW = 30.3592 1-4 EEL = 564.8863 RESTRAINT = 55.4554 EAMBER = -311.5038 NSTEP ENERGY RMS GMAX NAME NUMBER 3700 -2.5606E+02 9.3199E-02 5.8291E-01 C 98 BOND = 11.4375 ANGLE = 77.5978 DIHED = 88.5844 VDWAALS = -56.5431 EEL = -688.9572 EGB = -338.8895 1-4 VDW = 30.3597 1-4 EEL = 564.9052 RESTRAINT = 55.4430 EAMBER = -311.5052 NSTEP ENERGY RMS GMAX NAME NUMBER 3750 -2.5607E+02 5.8137E-02 3.5942E-01 CG2 76 BOND = 11.4183 ANGLE = 77.5969 DIHED = 88.5674 VDWAALS = -56.5357 EEL = -689.0538 EGB = -338.8040 1-4 VDW = 30.3610 1-4 EEL = 564.9301 RESTRAINT = 55.4460 EAMBER = -311.5198 NSTEP ENERGY RMS GMAX NAME NUMBER 3800 -2.5608E+02 3.8735E-02 2.4819E-01 O2 233 BOND = 11.4326 ANGLE = 77.6141 DIHED = 88.5409 VDWAALS = -56.5432 EEL = -689.0773 EGB = -338.7589 1-4 VDW = 30.3559 1-4 EEL = 564.8946 RESTRAINT = 55.4591 EAMBER = -311.5413 NSTEP ENERGY RMS GMAX NAME NUMBER 3850 -2.5609E+02 3.3766E-02 2.0345E-01 CG 231 BOND = 11.4272 ANGLE = 77.6136 DIHED = 88.5306 VDWAALS = -56.5486 EEL = -689.1203 EGB = -338.7073 1-4 VDW = 30.3599 1-4 EEL = 564.8951 RESTRAINT = 55.4610 EAMBER = -311.5497 NSTEP ENERGY RMS GMAX NAME NUMBER 3900 -2.5609E+02 2.8827E-02 1.3548E-01 HB22 202 BOND = 11.4229 ANGLE = 77.6046 DIHED = 88.5321 VDWAALS = -56.5441 EEL = -689.1792 EGB = -338.6681 1-4 VDW = 30.3619 1-4 EEL = 564.9127 RESTRAINT = 55.4625 EAMBER = -311.5573 NSTEP ENERGY RMS GMAX NAME NUMBER 3950 -2.5610E+02 3.5182E-02 1.8127E-01 OE1 111 BOND = 11.4205 ANGLE = 77.5993 DIHED = 88.5270 VDWAALS = -56.5486 EEL = -689.2167 EGB = -338.6281 1-4 VDW = 30.3660 1-4 EEL = 564.9179 RESTRAINT = 55.4624 EAMBER = -311.5626 NSTEP ENERGY RMS GMAX NAME NUMBER 4000 -2.5611E+02 4.0290E-02 2.0437E-01 O 12 BOND = 11.4191 ANGLE = 77.5944 DIHED = 88.5205 VDWAALS = -56.5497 EEL = -689.2804 EGB = -338.5756 1-4 VDW = 30.3668 1-4 EEL = 564.9305 RESTRAINT = 55.4680 EAMBER = -311.5745 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 4000 -2.5611E+02 4.0290E-02 2.0437E-01 O 12 BOND = 11.4191 ANGLE = 77.5944 DIHED = 88.5205 VDWAALS = -56.5497 EEL = -689.2804 EGB = -338.5756 1-4 VDW = 30.3668 1-4 EEL = 564.9305 RESTRAINT = 55.4680 EAMBER = -311.5745 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 30.45 96.80 | Bond 0.02 0.05 | Angle 0.27 0.86 | Dihedral 0.69 2.19 | Shake 0.00 0.00 | Other 0.03 0.10 | ------------------------------ | Total 31.46 | Generalized Born CPU Time: | | Routine Sec % | ------------------------------------ | Radii Calc 3.95 12.56 | Diagonal Calc 6.22 19.79 | Off Diagonal Calc 20.20 64.20 | GBSA LCPO Calc 0.00 0.00 | --------------------------------- | Total 30.37 96.55 | Setup CPU time: 0.00 seconds | NonSetup CPU time: 31.46 seconds | Total CPU time: 31.46 seconds 0.01 hours | Setup wall time: 0 seconds | NonSetup wall time: 32 seconds | Total wall time: 32 seconds 0.01 hours