------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | Run on 10/31/2008 at 00:19:43 [-O]verwriting output File Assignments: | MDIN: equil4.in | MDOUT: equil4.out |INPCRD: equil3.rst | PARM: complex_AA1_POP_BOX.prmtop |RESTRT: equil4.rst | REFC: equil3.rst | MDVEL: mdvel | MDEN: mden | MDCRD: equil4.mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: Equilibration after density MD, restraining protein and ligand &cntrl imin=0, irest=1, ntx=5, nstlim=1, dt=0.002, cut=10, ntb=2, ntp=1, taup=2.0, ntc=2, ntf=2, ntpr=1000, ntwx=1000, ntt=3, gamma_ln=2.0, temp0=300.0, ntr=1, / Keep protein and ligand restrained 32.0 RES 79 341 END END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI 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 = 38.953 | New format PARM file being parsed. | Version = 1.000 Date = 10/25/08 Time = 00:28:55 NATOM = 84578 NTYPES = 19 NBONH = 78494 MBONA = 6046 NTHETH = 20048 MTHETA = 7395 NPHIH = 33035 MPHIA = 15321 NHPARM = 0 NPARM = 0 NNB = 174234 NRES = 23681 NBONA = 6046 NTHETA = 7395 NPHIA = 15321 NUMBND = 65 NUMANG = 130 NPTRA = 61 NATYP = 46 NPHB = 1 IFBOX = 1 NMXRS = 134 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 4736518 | Hollerith 531151 | Integer 2854143 | Max Pairs 6089616 | nblistReal 1014936 | nblist Int 2971669 | Total 93552 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1000, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 1000, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 2, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 10.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Molecular dynamics: nstlim = 1, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000 Pressure regulation: ntp = 1 pres0 = 1.00000, comp = 44.60000, taup = 2.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 109.339 Box Y = 101.215 Box Z = 77.906 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 120 NFFT2 = 108 NFFT3 = 80 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 | MPI Timing options: | profile_mpi = 0 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: Keep protein and ligand restrained GROUP 1 HAS HARMONIC CONSTRAINTS 32.00000 GRP 1 RES 79 TO 341 Number of atoms in this group = 4106 ----- READING GROUP 2; TITLE: END GROUP 2 HAS HARMONIC CONSTRAINTS 0.00000 rfree: End of file on unit 5