------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 12 | Run on 03/22/2019 at 08:41:09 [-O]verwriting output File Assignments: | MDIN: min.in | MDOUT: min.out | INPCRD: coords.inpcrd | PARM: coords.prmtop | RESTRT: min.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo Here is the input file: Minimize the system with GMIN &cntrl imin=1,maxcyc=1,ncyc=1,ntb=0,cut= 999.0,drms=0.000001, igb=2,saltcon=0.3, pencut=-0.001, nmropt=0, ntr=0, rgbmax = 25.0, ifswitch = 1, / | Conditional Compilation Defines Used: | New format PARM file being parsed. | Version = 1.000 Date = 02/11/19 Time = 11:57:31 | 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 = 446 NTYPES = 13 NBONH = 234 MBONA = 212 NTHETH = 537 MTHETA = 281 NPHIH = 1015 MPHIA = 910 NHPARM = 0 NPARM = 0 NNB = 2470 NRES = 27 NBONA = 212 NTHETA = 281 NPHIA = 910 NUMBND = 42 NUMANG = 93 NPTRA = 133 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 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 = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, 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 = 999.00000, intdiel = 1.00000 saltcon = 0.30000, 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 = 0 Energy minimization: maxcyc = 1, ncyc = 1, ntmin = 1 dx0 = 0.01000, drms = 0.00000 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 1 -------------------------------------------------------------------------------- 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 14896 | Integers 45262 -------------------------------------------------------------------------------- 4. RESULTS --------------------------------------------------------------------------------