------------------------------------------------------- Amber 16 SANDER 2016 ------------------------------------------------------- | Run on 02/20/2018 at 18:38:36 | Executable path: sander | Working directory: /home/Amber_DNA_QMMM/AAA_OPC/QMMM | Hostname: t7910 [-O]verwriting output File Assignments: | MDIN: AAA_salt_qmmm_orc.in | MDOUT: AAA_salt_qmmm_orc.out |INPCRD: inpcrd | PARM: AAA_salt.prmtop |RESTRT: AAA_salt_qmmm_orc.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: cgataaatagc : Frame 1000 QMMM test &cntrl imin=0, ntb=1 cut=8.0, ntc=2, ntf=2, tempi = 310.15, temp0 = 310.15, ntt = 3, gamma_ln = 1.0, nstlim=0, dt=0.002, ntpr=1, ntwx=1,ifqnt=1 / &qmmm qmmask=':5-7,16-18 | (:5-7,16-18 <:5.0 & :WAT) | (:5-7,16-18 <:9.0 & :Na+)', qmcharge=0, qm_theory='EXTERN', qmshake=0, qm_ewald=0, writepdb = 1 / &orc basis = 'sto-3g', method = 'hf', num_threads = 30 / -------------------------------------------------------------------------------- 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 = 23.124 | New format PARM file being parsed. | Version = 1.000 Date = 09/28/17 Time = 15:25:24 NATOM = 18490 NTYPES = 20 NBONH = 13552 MBONA = 4931 NTHETH = 597 MTHETA = 765 NPHIH = 1216 MPHIA = 1591 NHPARM = 0 NPARM = 0 NNB = 34968 NRES = 4515 NBONA = 4931 NTHETA = 765 NPHIA = 1591 NUMBND = 53 NUMANG = 103 NPTRA = 70 NATYP = 34 NPHB = 1 IFBOX = 2 NMXRS = 34 IFCAP = 0 NEXTRA = 4433 NCOPY = 0 | Memory Use Allocated | Real 1334892 | Hollerith 59987 | Integer 654067 | Max Pairs 7396000 | nblistReal 221880 | nblist Int 644835 | Total 46361 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 LOADING THE QUANTUM ATOMS AS GROUPS Mask :5-7,16-18 | (:5-7,16-18 <:5.0 & :WAT) | (:5-7,16-18 <:9.0 & :Na+); matches 17964 atoms PARAMETER RANGE CHECKING: parameter QMMM: (number of quantum atoms) has value 17964 This is outside the legal range Lower limit: 1 Upper limit: 10000 The limits may be adjustable; search in the .h files