------------------------------------------------------- Amber 16 SANDER 2016 ------------------------------------------------------- | Run on 06/28/2019 at 02:03:55 | Executable path: sander | Working directory: /home/srania/2bh9_ligand_amber/new/26_Jun | Hostname: Unknown [-O]verwriting output File Assignments: | MDIN: min_all.in | MDOUT: complex_min_all.out |INPCRD: complex.inpcrd | PARM: complex.prmtop |RESTRT: complex_min_all.rst | REFC: refc | MDVEL: mdvel | MDFRC: mdfrc | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj Here is the input file: Minimization of the entire molecular system &cntrl imin=1, maxcyc=2000, ntpr=5, &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 59.303 | New format PARM file being parsed. | Version = 1.000 Date = 06/26/19 Time = 11:01:35 NATOM = 143978 NTYPES = 34 NBONH = 139936 MBONA = 4135 NTHETH = 8999 MTHETA = 5606 NPHIH = 18285 MPHIA = 17482 NHPARM = 0 NPARM = 0 NNB = 225461 NRES = 45824 NBONA = 4135 NTHETA = 5606 NPHIA = 17482 NUMBND = 92 NUMANG = 202 NPTRA = 219 NATYP = 56 NPHB = 1 IFBOX = 1 NMXRS = 73 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 11320608 | Hollerith 477760 | Integer 5006599 | Max Pairs 47992666 | nblistReal 1727736 | nblist Int 7286810 | Total 339298 kbytes | 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. | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 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 = 5, 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 = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 2000, ncyc = 10, ntmin = 1 dx0 = 0.01000, drms = 0.00010 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 0 Box X = 118.606 Box Y = 118.869 Box Z = 118.654 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 120 NFFT2 = 120 NFFT3 = 120 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- default_name begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 45326 Sum of charges from parm topology file = -0.00100117 Forcing neutrality... -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION using 5000.0 points per unit in tabled values TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 26601265 | TOTAL SIZE OF NONBOND LIST = 26601265 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.1201E+05 1.1157E+02 4.7918E+04 HE1 7053 BOND = 392.1043 ANGLE = 1237.0895 DIHED = 6175.5171 VDWAALS = 52339.7450 EEL = -493250.3455 HBOND = 0.0000 1-4 VDW = 2578.3540 1-4 EEL = 18521.8536 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 5 -4.1493E+05 4.1469E+01 1.6127E+04 HE1 7053 BOND = 391.9099 ANGLE = 1236.3550 DIHED = 6175.4229 VDWAALS = 49504.8089 EEL = -493334.5627 HBOND = 0.0000 1-4 VDW = 2578.1468 1-4 EEL = 18521.6373 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 10 -4.1765E+05 1.5616E+01 2.4342E+03 HE1 7053 BOND = 402.3150 ANGLE = 1229.9237 DIHED = 6174.6112 VDWAALS = 47547.5728 EEL = -494099.6344 HBOND = 0.0000 1-4 VDW = 2576.1320 1-4 EEL = 18519.6151 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 15 -4.4437E+05 4.7595E+00 2.4953E+02 HB3 6420 BOND = 13548.1125 ANGLE = 1218.9589 DIHED = 6174.3042 VDWAALS = 42997.8279 EEL = -529213.5255 HBOND = 0.0000 1-4 VDW = 2490.9323 1-4 EEL = 18415.2070 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 20 -4.6223E+05 6.3525E+01 2.6113E+04 HG22 7310 BOND = 42931.6345 ANGLE = 1648.8344 DIHED = 6282.8854 VDWAALS = 45676.0475 EEL = -579106.3024 HBOND = 0.0000 1-4 VDW = 2227.3536 1-4 EEL = 18105.2601 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 25 1.7903E+07 6.0521E+05 2.7277E+08 CG2 4394 BOND = 138231.3991 ANGLE = 10176.6811 DIHED = 7716.9420 VDWAALS = 18066066.6134 EEL = -614341.9727 HBOND = 0.0000 1-4 VDW = 277617.3004 1-4 EEL = 17256.8810 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 30 1.7222E+07 5.7664E+05 2.5970E+08 CG2 4394 BOND = 138230.7732 ANGLE = 10176.6357 DIHED = 7716.9429 VDWAALS = 17385498.1326 EEL = -614341.8893 HBOND = 0.0000 1-4 VDW = 277507.6838 1-4 EEL = 17256.8798 RESTRAINT = 0.0000