possible FAILURE:  check tp3.mdout.dif
/home/progs/amber20/AmberTools/test/leap/OL3
15,83c15,16
<  NATOM  =    7622 NTYPES =      17 NBONH =    7537 MBONA  =      91
<  NTHETH =     102 MTHETA =     140 NPHIH =     227 MPHIA  =     277
<  NHPARM =       0 NPARM  =       0 NNB   =   10697 NRES   =    2504
<  NBONA  =      91 NTHETA =     140 NPHIA =     277 NUMBND =      43
<  NUMANG =      82 NPTRA  =      56 NATYP =      29 NPHB   =       1
<  IFBOX  =       2 NMXRS  =      33 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<      BOX TYPE: TRUNCATED OCTAHEDRON
< --------------------------------------------------------------------------------
<    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     =       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  =       1, 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 =   48.550   Box Y =   48.550   Box Z =   48.550
<      Alpha =  109.471   Beta  =  109.471   Gamma =  109.471
<      NFFT1 =   48       NFFT2 =   48       NFFT3 =   48
<      Cutoff=    8.000   Tol   =0.100E-4
<      Ewald Coefficient =  0.34864
<      Interpolation order =    4
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< default_name
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:     2497
<      Sum of charges from parm topology file =   0.
<      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. to cutoff
<  ---------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.3090E+5     1.0246E+4     5.8004E+5     O        5997
<  BOND    =       31.0886  ANGLE   =       63.0595  DIHED      =       96.6741
<  VDWAALS =   155288.6411  EEL     =   -24073.4065  HBOND      =        0.
<  1-4 VDW =       40.2747  1-4 EEL =     -549.4989  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.3090E+5     1.0246E+4     5.8004E+5     O        5997
<  BOND    =       31.0886  ANGLE   =       63.0595  DIHED      =       96.6741
<  VDWAALS =   155288.6411  EEL     =   -24073.4065  HBOND      =        0.
<  1-4 VDW =       40.2747  1-4 EEL =     -549.4989  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---
> ERROR: I could not find the number of atoms or the time on
>        the second line of your inpcrd file [rGACC.nomin.rst7]. Bad INPCRD file!
---------------------------------------
possible FAILURE:  check mdout.dif
/home/progs/amber20/AmberTools/test/leap/OL3
14,73d13
<  NATOM  =     128 NTYPES =      14 NBONH =      46 MBONA  =      91
<  NTHETH =     102 MTHETA =     140 NPHIH =     227 MPHIA  =     277
<  NHPARM =       0 NPARM  =       0 NNB   =     706 NRES   =       4
<  NBONA  =      91 NTHETA =     140 NPHIA =     277 NUMBND =      41
<  NUMANG =      82 NPTRA  =      56 NATYP =      26 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      33 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  Implicit solvent radii are modified Bondi radii (mbondi)
< --------------------------------------------------------------------------------
<    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     =       2, ntb     =       0, igb     =       1, nsnb    =      25
<      ipol    =       0, gbsa    =       0, iesp    =       0
<      dielc   =   1.00000, cut     =9999.00000, intdiel =   1.00000
<      saltcon =   0., offset  =   0.09000, gbalpha=    1.00000
<      gbbeta  =   0., gbgamma =   0., surften =   0.00500
<      rdt     =   0., rgbmax  =  25.00000  extdiel =  78.50000
<      alpb  =        0
< Frozen or restrained atoms:
<      ibelly  =       0, ntr     =       0
< Energy minimization:
<      maxcyc  =       1, ncyc    =      10, ntmin   =       1
<      dx0     =   0.01000, drms    =   0.00010
< SHAKE:
<      ntc     =       2, jfastw  =       0
<      tol     =   0.00001
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< default_name
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:        0
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1      -7.7121E+2     2.0991E+1     6.9661E+1     N1        109
<  BOND    =       30.9686  ANGLE   =       63.0583  DIHED      =       96.6742
<  VDWAALS =      -45.0874  EEL     =      -69.4993  EGB        =     -338.1099
<  1-4 VDW =       40.2769  1-4 EEL =     -549.4863  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1      -7.7121E+2     2.0991E+1     6.9661E+1     N1        109
<  BOND    =       30.9686  ANGLE   =       63.0583  DIHED      =       96.6742
<  VDWAALS =      -45.0874  EEL     =      -69.4993  EGB        =     -338.1099
<  1-4 VDW =       40.2769  1-4 EEL =     -549.4863  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---------------------------------------
possible FAILURE:  check tp3.mdout.dif
/home/progs/amber20/AmberTools/test/leap/Yildirim
15,83c15,16
<  NATOM  =    7622 NTYPES =      17 NBONH =    7537 MBONA  =      91
<  NTHETH =     102 MTHETA =     140 NPHIH =     227 MPHIA  =     289
<  NHPARM =       0 NPARM  =       0 NNB   =   10697 NRES   =    2504
<  NBONA  =      91 NTHETA =     140 NPHIA =     289 NUMBND =      43
<  NUMANG =      82 NPTRA  =      68 NATYP =      30 NPHB   =       1
<  IFBOX  =       2 NMXRS  =      33 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<      BOX TYPE: TRUNCATED OCTAHEDRON
< --------------------------------------------------------------------------------
<    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     =       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  =       1, 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 =   48.550   Box Y =   48.550   Box Z =   48.550
<      Alpha =  109.471   Beta  =  109.471   Gamma =  109.471
<      NFFT1 =   48       NFFT2 =   48       NFFT3 =   48
<      Cutoff=    8.000   Tol   =0.100E-4
<      Ewald Coefficient =  0.34864
<      Interpolation order =    4
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< default_name
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:     2497
<      Sum of charges from parm topology file =   0.
<      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. to cutoff
<  ---------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.3091E+5     1.0246E+4     5.8004E+5     O        5997
<  BOND    =       31.0886  ANGLE   =       63.0595  DIHED      =      111.9706
<  VDWAALS =   155288.6411  EEL     =   -24073.4065  HBOND      =        0.
<  1-4 VDW =       40.2747  1-4 EEL =     -549.4989  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.3091E+5     1.0246E+4     5.8004E+5     O        5997
<  BOND    =       31.0886  ANGLE   =       63.0595  DIHED      =      111.9706
<  VDWAALS =   155288.6411  EEL     =   -24073.4065  HBOND      =        0.
<  1-4 VDW =       40.2747  1-4 EEL =     -549.4989  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---
> ERROR: I could not find the number of atoms or the time on
>        the second line of your inpcrd file [rGACC.nomin.rst7]. Bad INPCRD file!
---------------------------------------
possible FAILURE:  check mdout.dif
/home/progs/amber20/AmberTools/test/leap/Yildirim
14,73d13
<  NATOM  =     128 NTYPES =      14 NBONH =      46 MBONA  =      91
<  NTHETH =     102 MTHETA =     140 NPHIH =     227 MPHIA  =     289
<  NHPARM =       0 NPARM  =       0 NNB   =     706 NRES   =       4
<  NBONA  =      91 NTHETA =     140 NPHIA =     289 NUMBND =      41
<  NUMANG =      82 NPTRA  =      68 NATYP =      27 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      33 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  Implicit solvent radii are modified Bondi radii (mbondi)
< --------------------------------------------------------------------------------
<    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     =       2, ntb     =       0, igb     =       1, nsnb    =      25
<      ipol    =       0, gbsa    =       0, iesp    =       0
<      dielc   =   1.00000, cut     =9999.00000, intdiel =   1.00000
<      saltcon =   0., offset  =   0.09000, gbalpha=    1.00000
<      gbbeta  =   0., gbgamma =   0., surften =   0.00500
<      rdt     =   0., rgbmax  =  25.00000  extdiel =  78.50000
<      alpb  =        0
< Frozen or restrained atoms:
<      ibelly  =       0, ntr     =       0
< Energy minimization:
<      maxcyc  =       1, ncyc    =      10, ntmin   =       1
<      dx0     =   0.01000, drms    =   0.00010
< SHAKE:
<      ntc     =       2, jfastw  =       0
<      tol     =   0.00001
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< default_name
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:        0
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1      -7.5591E+2     2.1015E+1     7.1190E+1     N1        109
<  BOND    =       30.9686  ANGLE   =       63.0583  DIHED      =      111.9697
<  VDWAALS =      -45.0874  EEL     =      -69.4993  EGB        =     -338.1099
<  1-4 VDW =       40.2769  1-4 EEL =     -549.4863  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1      -7.5591E+2     2.1015E+1     7.1190E+1     N1        109
<  BOND    =       30.9686  ANGLE   =       63.0583  DIHED      =      111.9697
<  VDWAALS =      -45.0874  EEL     =      -69.4993  EGB        =     -338.1099
<  1-4 VDW =       40.2769  1-4 EEL =     -549.4863  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---------------------------------------
possible FAILURE:  check rGACU.out.dif
/home/progs/amber20/AmberTools/test/leap/Yildirim
14,70d13
<  NATOM  =     128 NTYPES =      14 NBONH =      43 MBONA  =      94
<  NTHETH =      99 MTHETA =     144 NPHIH =     221 MPHIA  =     293
<  NHPARM =       0 NPARM  =       0 NNB   =     706 NRES   =       4
<  NBONA  =      94 NTHETA =     144 NPHIA =     293 NUMBND =      44
<  NUMANG =      91 NPTRA  =      78 NATYP =      28 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      34 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  Implicit solvent radii are modified Bondi radii (mbondi)
< --------------------------------------------------------------------------------
<    2.  CONTROL  DATA  FOR  THE  RUN
< --------------------------------------------------------------------------------
< G
< 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     =       1, nsnb    =      25
<      ipol    =       0, gbsa    =       0, iesp    =       0
<      dielc   =   1.00000, cut     =9999.00000, intdiel =   1.00000
<      saltcon =   0., offset  =   0.09000, gbalpha=    1.00000
<      gbbeta  =   0., gbgamma =   0., surften =   0.00500
<      rdt     =   0., rgbmax  =  25.00000  extdiel =  78.50000
<      alpb  =        0
< Frozen or restrained atoms:
<      ibelly  =       0, ntr     =       0
< Energy minimization:
<      maxcyc  =       1, ncyc    =      10, ntmin   =       1
<      dx0     =   0.01000, drms    =   0.00010
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< G
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:        0
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       2.1210E+3     9.1328E+2     7.0908E+3     H3'        29
<  BOND    =       10.9713  ANGLE   =      143.2326  DIHED      =      107.6871
<  VDWAALS =     2631.2852  EEL     =       66.8146  EGB        =     -558.8739
<  1-4 VDW =       94.3799  1-4 EEL =     -374.4818  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       2.1210E+3     9.1328E+2     7.0908E+3     H3'        29
<  BOND    =       10.9713  ANGLE   =      143.2326  DIHED      =      107.6871
<  VDWAALS =     2631.2852  EEL     =       66.8146  EGB        =     -558.8739
<  1-4 VDW =       94.3799  1-4 EEL =     -374.4818  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---------------------------------------
possible FAILURE:  check bsc1.mdout.dif
/home/progs/amber20/AmberTools/test/leap/4PY5
14,73d13
<  NATOM  =    5555 NTYPES =      17 NBONH =    2669 MBONA  =    3005
<  NTHETH =    6152 MTHETA =    4207 NPHIH =   12018 MPHIA  =   11596
<  NHPARM =       0 NPARM  =       0 NNB   =   30944 NRES   =     305
<  NBONA  =    3005 NTHETA =    4207 NPHIA =   11596 NUMBND =     118
<  NUMANG =     271 NPTRA  =     259 NATYP =      47 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      34 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  Implicit solvent radii are modified Bondi radii (mbondi)
< --------------------------------------------------------------------------------
<    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     =       2, ntb     =       0, igb     =       5, nsnb    =      25
<      ipol    =       0, gbsa    =       0, iesp    =       0
<      dielc   =   1.00000, cut     =9999.00000, intdiel =   1.00000
<      saltcon =   0., offset  =   0.09000, gbalpha=    1.00000
<      gbbeta  =   0.80000, gbgamma =   4.85000, surften =   0.00500
<      rdt     =   0., rgbmax  =  25.00000  extdiel =  78.50000
<      alpb  =        0
< Frozen or restrained atoms:
<      ibelly  =       0, ntr     =       0
< Energy minimization:
<      maxcyc  =       1, ncyc    =      10, ntmin   =       1
<      dx0     =   0.01000, drms    =   0.00010
< SHAKE:
<      ntc     =       2, jfastw  =       0
<      tol     =   0.00001
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< default_name
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:        0
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1      -1.4039E+4     2.4056E+1     1.3132E+3     HD3      1903
<  BOND    =      128.1173  ANGLE   =     1510.4159  DIHED      =     3790.6522
<  VDWAALS =    -2183.9043  EEL     =   -16555.6955  EGB        =   -11583.1716
<  1-4 VDW =     1700.5831  1-4 EEL =     9153.5036  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1      -1.4039E+4     2.4056E+1     1.3132E+3     HD3      1903
<  BOND    =      128.1173  ANGLE   =     1510.4159  DIHED      =     3790.6522
<  VDWAALS =    -2183.9043  EEL     =   -16555.6955  EGB        =   -11583.1716
<  1-4 VDW =     1700.5831  1-4 EEL =     9153.5036  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---------------------------------------
possible FAILURE:  check mdout.dif
/home/progs/amber20/AmberTools/test/leap/BSC0
14,70d13
<  NATOM  =     758 NTYPES =      15 NBONH =     272 MBONA  =     544
<  NTHETH =     640 MTHETA =     836 NPHIH =    1366 MPHIA  =    1544
<  NHPARM =       0 NPARM  =       0 NNB   =    4210 NRES   =      24
<  NBONA  =     544 NTHETA =     836 NPHIA =    1544 NUMBND =      41
<  NUMANG =      86 NPTRA  =      49 NATYP =      26 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      34 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  Implicit solvent radii are modified Bondi radii (mbondi)
< --------------------------------------------------------------------------------
<    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     =       1, nsnb    =      25
<      ipol    =       0, gbsa    =       0, iesp    =       0
<      dielc   =   1.00000, cut     =9999.00000, intdiel =   1.00000
<      saltcon =   0., offset  =   0.09000, gbalpha=    1.00000
<      gbbeta  =   0., gbgamma =   0., surften =   0.00500
<      rdt     =   0., rgbmax  =  25.00000  extdiel =  78.50000
<      alpb  =        0
< Frozen or restrained atoms:
<      ibelly  =       0, ntr     =       0
< Energy minimization:
<      maxcyc  =       1, ncyc    =      10, ntmin   =       1
<      dx0     =   0.01000, drms    =   0.00010
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< default_name
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:        0
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1      -4.6839E+3     2.5649E+1     4.8351E+2     O3'       378
<  BOND    =      435.3447  ANGLE   =      119.6743  DIHED      =      458.3505
<  VDWAALS =     -269.1507  EEL     =     3589.8578  EGB        =    -6179.6957
<  1-4 VDW =      215.2408  1-4 EEL =    -3053.5631  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1      -4.6839E+3     2.5649E+1     4.8351E+2     O3'       378
<  BOND    =      435.3447  ANGLE   =      119.6743  DIHED      =      458.3505
<  VDWAALS =     -269.1507  EEL     =     3589.8578  EGB        =    -6179.6957
<  1-4 VDW =      215.2408  1-4 EEL =    -3053.5631  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---------------------------------------
possible FAILURE:  check mdout.dif
/home/progs/amber20/AmberTools/test/leap/BSC1
14,70d13
<  NATOM  =     758 NTYPES =      15 NBONH =     272 MBONA  =     544
<  NTHETH =     640 MTHETA =     836 NPHIH =    1274 MPHIA  =    1606
<  NHPARM =       0 NPARM  =       0 NNB   =    4210 NRES   =      24
<  NBONA  =     544 NTHETA =     836 NPHIA =    1606 NUMBND =      50
<  NUMANG =     103 NPTRA  =      66 NATYP =      29 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      34 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  Implicit solvent radii are modified Bondi radii (mbondi)
< --------------------------------------------------------------------------------
<    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     =       1, nsnb    =      25
<      ipol    =       0, gbsa    =       0, iesp    =       0
<      dielc   =   1.00000, cut     =9999.00000, intdiel =   1.00000
<      saltcon =   0., offset  =   0.09000, gbalpha=    1.00000
<      gbbeta  =   0., gbgamma =   0., surften =   0.00500
<      rdt     =   0., rgbmax  =  25.00000  extdiel =  78.50000
<      alpb  =        0
< Frozen or restrained atoms:
<      ibelly  =       0, ntr     =       0
< Energy minimization:
<      maxcyc  =       1, ncyc    =      10, ntmin   =       1
<      dx0     =   0.01000, drms    =   0.00010
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< default_name
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:        0
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1      -4.5867E+3     2.5683E+1     4.8226E+2     O3'       378
<  BOND    =      435.3447  ANGLE   =      119.6743  DIHED      =      555.5500
<  VDWAALS =     -269.1507  EEL     =     3589.8578  EGB        =    -6179.6957
<  1-4 VDW =      215.2408  1-4 EEL =    -3053.5631  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1      -4.5867E+3     2.5683E+1     4.8226E+2     O3'       378
<  BOND    =      435.3447  ANGLE   =      119.6743  DIHED      =      555.5500
<  VDWAALS =     -269.1507  EEL     =     3589.8578  EGB        =    -6179.6957
<  1-4 VDW =      215.2408  1-4 EEL =    -3053.5631  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---------------------------------------
possible FAILURE:  check mdout.dif
/home/progs/amber20/AmberTools/test/leap/OL15
14,70d13
<  NATOM  =     758 NTYPES =      15 NBONH =     272 MBONA  =     544
<  NTHETH =     640 MTHETA =     836 NPHIH =    1390 MPHIA  =    1756
<  NHPARM =       0 NPARM  =       0 NNB   =    4210 NRES   =      24
<  NBONA  =     544 NTHETA =     836 NPHIA =    1756 NUMBND =      50
<  NUMANG =     103 NPTRA  =      71 NATYP =      29 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      34 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  Implicit solvent radii are modified Bondi radii (mbondi)
< --------------------------------------------------------------------------------
<    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     =       1, nsnb    =      25
<      ipol    =       0, gbsa    =       0, iesp    =       0
<      dielc   =   1.00000, cut     =9999.00000, intdiel =   1.00000
<      saltcon =   0., offset  =   0.09000, gbalpha=    1.00000
<      gbbeta  =   0., gbgamma =   0., surften =   0.00500
<      rdt     =   0., rgbmax  =  25.00000  extdiel =  78.50000
<      alpb  =        0
< Frozen or restrained atoms:
<      ibelly  =       0, ntr     =       0
< Energy minimization:
<      maxcyc  =       1, ncyc    =      10, ntmin   =       1
<      dx0     =   0.01000, drms    =   0.00010
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< default_name
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:        0
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1      -4.4985E+3     2.5650E+1     4.8351E+2     O3'       378
<  BOND    =      435.3447  ANGLE   =      119.6743  DIHED      =      643.7947
<  VDWAALS =     -269.1507  EEL     =     3589.8578  EGB        =    -6179.6957
<  1-4 VDW =      215.2408  1-4 EEL =    -3053.5631  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1      -4.4985E+3     2.5650E+1     4.8351E+2     O3'       378
<  BOND    =      435.3447  ANGLE   =      119.6743  DIHED      =      643.7947
<  VDWAALS =     -269.1507  EEL     =     3589.8578  EGB        =    -6179.6957
<  1-4 VDW =      215.2408  1-4 EEL =    -3053.5631  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---------------------------------------
possible FAILURE:  check bondi.out.dif
/home/progs/amber20/AmberTools/test/leap/pbradii
14,70d13
<  NATOM  =     320 NTYPES =      14 NBONH =     155 MBONA  =     170
<  NTHETH =     351 MTHETA =     230 NPHIH =     721 MPHIA  =     698
<  NHPARM =       0 NPARM  =       0 NNB   =    1749 NRES   =      20
<  NBONA  =     170 NTHETA =     230 NPHIA =     698 NUMBND =      62
<  NUMANG =     146 NPTRA  =     180 NATYP =      31 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  Implicit solvent radii are Bondi radii (bondi)
< --------------------------------------------------------------------------------
<    2.  CONTROL  DATA  FOR  THE  RUN
< --------------------------------------------------------------------------------
< ACE
< 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     =       1, nsnb    =      25
<      ipol    =       0, gbsa    =       0, iesp    =       0
<      dielc   =   1.00000, cut     =9999.00000, intdiel =   1.00000
<      saltcon =   0., offset  =   0.09000, gbalpha=    1.00000
<      gbbeta  =   0., gbgamma =   0., surften =   0.00500
<      rdt     =   0., rgbmax  =  25.00000  extdiel =  78.50000
<      alpb  =        0
< Frozen or restrained atoms:
<      ibelly  =       0, ntr     =       0
< Energy minimization:
<      maxcyc  =       1, ncyc    =      10, ntmin   =       1
<      dx0     =   0.01000, drms    =   0.00010
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< ACE
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:        0
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.0319E+8     8.4829E+7     1.5372E+9     OD1       173
<  BOND    =       13.2244  ANGLE   =       43.5454  DIHED      =      208.7532
<  VDWAALS = *************  EEL     =    -1213.7690  EGB        =     -477.5176
<  1-4 VDW =      112.1895  1-4 EEL =      841.0921  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.0319E+8     8.4829E+7     1.5372E+9     OD1       173
<  BOND    =       13.2244  ANGLE   =       43.5454  DIHED      =      208.7532
<  VDWAALS = *************  EEL     =    -1213.7690  EGB        =     -477.5176
<  1-4 VDW =      112.1895  1-4 EEL =      841.0921  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---------------------------------------
possible FAILURE:  check amber6.out.dif
/home/progs/amber20/AmberTools/test/leap/pbradii
14,70d13
<  NATOM  =     320 NTYPES =      14 NBONH =     155 MBONA  =     170
<  NTHETH =     351 MTHETA =     230 NPHIH =     721 MPHIA  =     698
<  NHPARM =       0 NPARM  =       0 NNB   =    1749 NRES   =      20
<  NBONA  =     170 NTHETA =     230 NPHIA =     698 NUMBND =      62
<  NUMANG =     146 NPTRA  =     180 NATYP =      31 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  Implicit solvent radii are amber6 modified Bondi radii (amber6)
< --------------------------------------------------------------------------------
<    2.  CONTROL  DATA  FOR  THE  RUN
< --------------------------------------------------------------------------------
< ACE
< 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     =       1, nsnb    =      25
<      ipol    =       0, gbsa    =       0, iesp    =       0
<      dielc   =   1.00000, cut     =9999.00000, intdiel =   1.00000
<      saltcon =   0., offset  =   0.09000, gbalpha=    1.00000
<      gbbeta  =   0., gbgamma =   0., surften =   0.00500
<      rdt     =   0., rgbmax  =  25.00000  extdiel =  78.50000
<      alpb  =        0
< Frozen or restrained atoms:
<      ibelly  =       0, ntr     =       0
< Energy minimization:
<      maxcyc  =       1, ncyc    =      10, ntmin   =       1
<      dx0     =   0.01000, drms    =   0.00010
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< ACE
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:        0
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.0319E+8     8.4829E+7     1.5372E+9     OD1       173
<  BOND    =       13.2244  ANGLE   =       43.5454  DIHED      =      208.7532
<  VDWAALS = *************  EEL     =    -1213.7690  EGB        =     -472.5615
<  1-4 VDW =      112.1895  1-4 EEL =      841.0921  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.0319E+8     8.4829E+7     1.5372E+9     OD1       173
<  BOND    =       13.2244  ANGLE   =       43.5454  DIHED      =      208.7532
<  VDWAALS = *************  EEL     =    -1213.7690  EGB        =     -472.5615
<  1-4 VDW =      112.1895  1-4 EEL =      841.0921  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---------------------------------------
possible FAILURE:  check mbondi.out.dif
/home/progs/amber20/AmberTools/test/leap/pbradii
14,70d13
<  NATOM  =     320 NTYPES =      14 NBONH =     155 MBONA  =     170
<  NTHETH =     351 MTHETA =     230 NPHIH =     721 MPHIA  =     698
<  NHPARM =       0 NPARM  =       0 NNB   =    1749 NRES   =      20
<  NBONA  =     170 NTHETA =     230 NPHIA =     698 NUMBND =      62
<  NUMANG =     146 NPTRA  =     180 NATYP =      31 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  Implicit solvent radii are modified Bondi radii (mbondi)
< --------------------------------------------------------------------------------
<    2.  CONTROL  DATA  FOR  THE  RUN
< --------------------------------------------------------------------------------
< ACE
< 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     =       1, nsnb    =      25
<      ipol    =       0, gbsa    =       0, iesp    =       0
<      dielc   =   1.00000, cut     =9999.00000, intdiel =   1.00000
<      saltcon =   0., offset  =   0.09000, gbalpha=    1.00000
<      gbbeta  =   0., gbgamma =   0., surften =   0.00500
<      rdt     =   0., rgbmax  =  25.00000  extdiel =  78.50000
<      alpb  =        0
< Frozen or restrained atoms:
<      ibelly  =       0, ntr     =       0
< Energy minimization:
<      maxcyc  =       1, ncyc    =      10, ntmin   =       1
<      dx0     =   0.01000, drms    =   0.00010
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< ACE
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:        0
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.0319E+8     8.4829E+7     1.5372E+9     OD1       173
<  BOND    =       13.2244  ANGLE   =       43.5454  DIHED      =      208.7532
<  VDWAALS = *************  EEL     =    -1213.7690  EGB        =     -458.5661
<  1-4 VDW =      112.1895  1-4 EEL =      841.0921  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.0319E+8     8.4829E+7     1.5372E+9     OD1       173
<  BOND    =       13.2244  ANGLE   =       43.5454  DIHED      =      208.7532
<  VDWAALS = *************  EEL     =    -1213.7690  EGB        =     -458.5661
<  1-4 VDW =      112.1895  1-4 EEL =      841.0921  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---------------------------------------
possible FAILURE:  check mbondi2.out.dif
/home/progs/amber20/AmberTools/test/leap/pbradii
14,70d13
<  NATOM  =     320 NTYPES =      14 NBONH =     155 MBONA  =     170
<  NTHETH =     351 MTHETA =     230 NPHIH =     721 MPHIA  =     698
<  NHPARM =       0 NPARM  =       0 NNB   =    1749 NRES   =      20
<  NBONA  =     170 NTHETA =     230 NPHIA =     698 NUMBND =      62
<  NUMANG =     146 NPTRA  =     180 NATYP =      31 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
< --------------------------------------------------------------------------------
< ACE
< 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     =       1, nsnb    =      25
<      ipol    =       0, gbsa    =       0, iesp    =       0
<      dielc   =   1.00000, cut     =9999.00000, intdiel =   1.00000
<      saltcon =   0., offset  =   0.09000, gbalpha=    1.00000
<      gbbeta  =   0., gbgamma =   0., surften =   0.00500
<      rdt     =   0., rgbmax  =  25.00000  extdiel =  78.50000
<      alpb  =        0
< Frozen or restrained atoms:
<      ibelly  =       0, ntr     =       0
< Energy minimization:
<      maxcyc  =       1, ncyc    =      10, ntmin   =       1
<      dx0     =   0.01000, drms    =   0.00010
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< ACE
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:        0
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.0319E+8     8.4829E+7     1.5372E+9     OD1       173
<  BOND    =       13.2244  ANGLE   =       43.5454  DIHED      =      208.7532
<  VDWAALS = *************  EEL     =    -1213.7690  EGB        =     -463.3623
<  1-4 VDW =      112.1895  1-4 EEL =      841.0921  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.0319E+8     8.4829E+7     1.5372E+9     OD1       173
<  BOND    =       13.2244  ANGLE   =       43.5454  DIHED      =      208.7532
<  VDWAALS = *************  EEL     =    -1213.7690  EGB        =     -463.3623
<  1-4 VDW =      112.1895  1-4 EEL =      841.0921  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---------------------------------------
possible FAILURE:  check parse.out.dif
/home/progs/amber20/AmberTools/test/leap/pbradii
14,70d13
<  NATOM  =     320 NTYPES =      14 NBONH =     155 MBONA  =     170
<  NTHETH =     351 MTHETA =     230 NPHIH =     721 MPHIA  =     698
<  NHPARM =       0 NPARM  =       0 NNB   =    1749 NRES   =      20
<  NBONA  =     170 NTHETA =     230 NPHIA =     698 NUMBND =      62
<  NUMANG =     146 NPTRA  =     180 NATYP =      31 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  Implicit solvent radii are Parse radii (parse)
< --------------------------------------------------------------------------------
<    2.  CONTROL  DATA  FOR  THE  RUN
< --------------------------------------------------------------------------------
< ACE
< 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     =       1, nsnb    =      25
<      ipol    =       0, gbsa    =       0, iesp    =       0
<      dielc   =   1.00000, cut     =9999.00000, intdiel =   1.00000
<      saltcon =   0., offset  =   0.09000, gbalpha=    1.00000
<      gbbeta  =   0., gbgamma =   0., surften =   0.00500
<      rdt     =   0., rgbmax  =  25.00000  extdiel =  78.50000
<      alpb  =        0
< Frozen or restrained atoms:
<      ibelly  =       0, ntr     =       0
< Energy minimization:
<      maxcyc  =       1, ncyc    =      10, ntmin   =       1
<      dx0     =   0.01000, drms    =   0.00010
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< ACE
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:        0
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.0319E+8     8.4829E+7     1.5372E+9     OD1       173
<  BOND    =       13.2244  ANGLE   =       43.5454  DIHED      =      208.7532
<  VDWAALS = *************  EEL     =    -1213.7690  EGB        =     -964.6706
<  1-4 VDW =      112.1895  1-4 EEL =      841.0921  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.0319E+8     8.4829E+7     1.5372E+9     OD1       173
<  BOND    =       13.2244  ANGLE   =       43.5454  DIHED      =      208.7532
<  VDWAALS = *************  EEL     =    -1213.7690  EGB        =     -964.6706
<  1-4 VDW =      112.1895  1-4 EEL =      841.0921  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---------------------------------------
possible FAILURE:  check mbondi3.out.dif
/home/progs/amber20/AmberTools/test/leap/pbradii
14,70d13
<  NATOM  =     320 NTYPES =      14 NBONH =     155 MBONA  =     170
<  NTHETH =     351 MTHETA =     230 NPHIH =     721 MPHIA  =     698
<  NHPARM =       0 NPARM  =       0 NNB   =    1749 NRES   =      20
<  NBONA  =     170 NTHETA =     230 NPHIA =     698 NUMBND =      62
<  NUMANG =     146 NPTRA  =     180 NATYP =      31 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  Implicit solvent radii are ArgH and AspGluO modified Bondi2 radii (mbondi3)
< --------------------------------------------------------------------------------
<    2.  CONTROL  DATA  FOR  THE  RUN
< --------------------------------------------------------------------------------
< ACE
< 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     =       1, nsnb    =      25
<      ipol    =       0, gbsa    =       0, iesp    =       0
<      dielc   =   1.00000, cut     =9999.00000, intdiel =   1.00000
<      saltcon =   0., offset  =   0.09000, gbalpha=    1.00000
<      gbbeta  =   0., gbgamma =   0., surften =   0.00500
<      rdt     =   0., rgbmax  =  25.00000  extdiel =  78.50000
<      alpb  =        0
< Frozen or restrained atoms:
<      ibelly  =       0, ntr     =       0
< Energy minimization:
<      maxcyc  =       1, ncyc    =      10, ntmin   =       1
<      dx0     =   0.01000, drms    =   0.00010
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< ACE
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:        0
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.0319E+8     8.4829E+7     1.5372E+9     OD1       173
<  BOND    =       13.2244  ANGLE   =       43.5454  DIHED      =      208.7532
<  VDWAALS = *************  EEL     =    -1213.7690  EGB        =     -484.7888
<  1-4 VDW =      112.1895  1-4 EEL =      841.0921  RESTRAINT  =        0.
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1       1.0319E+8     8.4829E+7     1.5372E+9     OD1       173
<  BOND    =       13.2244  ANGLE   =       43.5454  DIHED      =      208.7532
<  VDWAALS = *************  EEL     =    -1213.7690  EGB        =     -484.7888
<  1-4 VDW =      112.1895  1-4 EEL =      841.0921  RESTRAINT  =        0.
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---------------------------------------
possible FAILURE: (ignored)  check parmff14SB_1okl.prm.dif
/home/progs/amber20/AmberTools/test/pymsmt/amb2chm_par
1603c1603
< cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 0.833333333333 wmin 1.5
---
> cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 0.8333333333333334 wmin 1.5
---------------------------------------
possible FAILURE:  check mdout.dhfr.noboxinfo.dif
/home/progs/amber20/test/dhfr
19a20,21
> ERROR: I could not find the number of atoms or the time on
>        the second line of your inpcrd file [md12noboxinfo.x]. Bad INPCRD file!
---------------------------------------
possible FAILURE:  check nc_headers.dif
/home/progs/amber20/test/bintraj
1,31d0
< netcdf mdtrj {
< dimensions:
< 	frame = UNLIMITED ; // (10 currently)
< 	spatial = 3 ;
< 	atom = 28 ;
< 	cell_spatial = 3 ;
< 	label = 5 ;
< 	cell_angular = 3 ;
< variables:
< 	float time(frame) ;
< 		time:units = "picosecond" ;
< 	char spatial(spatial) ;
< 	float coordinates(frame, atom, spatial) ;
< 		coordinates:units = "angstrom" ;
< 	float velocities(frame, atom, spatial) ;
< 		velocities:units = "angstrom/picosecond" ;
< 		velocities:scale_factor = 20.455 ;
< 	char cell_spatial(cell_spatial) ;
< 	char cell_angular(cell_angular, label) ;
< 	double cell_lengths(frame, cell_spatial) ;
< 		cell_lengths:units = "angstrom" ;
< 	double cell_angles(frame, cell_angular) ;
< 		cell_angles:units = "degree" ;
< // global attributes:
< 		:title = "netCDF output test" ;
< 		:application = "AMBER" ;
< 		:program = "sander" ;
< 		:programVersion = "20.0" ;
< 		:Conventions = "AMBER" ;
< 		:ConventionVersion = "1.0" ;
< }
---------------------------------------
possible FAILURE: (ignored)  check emap2.out.dif
/home/progs/amber20/test/emap2
24,885d23
<  NATOM  =    4278 NTYPES =      14 NBONH =    1442 MBONA  =    3174
<  NTHETH =    3290 MTHETA =    4952 NPHIH =    6954 MPHIA  =    9536
<  NHPARM =       0 NPARM  =       0 NNB   =   23892 NRES   =     132
<  NBONA  =    3174 NTHETA =    4952 NPHIA =    9536 NUMBND =      46
<  NUMANG =      94 NPTRA  =      61 NATYP =      27 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      35 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  Implicit solvent radii are modified Bondi radii (mbondi)
< --------------------------------------------------------------------------------
<    2.  CONTROL  DATA  FOR  THE  RUN
< --------------------------------------------------------------------------------
< General flags:
<      imin    =       1, nmropt  =       1
< Nature and format of input:
<      ntx     =       1, irest   =       0, ntrx    =       1
< Nature and format of output:
<      ntxo    =       1, 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     =       2, ntb     =       0, igb     =       1, nsnb    =      25
<      ipol    =       0, gbsa    =       0, iesp    =       0
<      dielc   =   1.00000, cut     =   9.00000, intdiel =   1.00000
<      saltcon =   0., offset  =   0.09000, gbalpha=    1.00000
<      gbbeta  =   0., gbgamma =   0., surften =   0.00500
<      rdt     =   0., rgbmax  =  25.00000  extdiel =  78.50000
<      alpb  =        0
< Frozen or restrained atoms:
<      ibelly  =       0, ntr     =       0
< Energy minimization:
<      maxcyc  =       0, ncyc    =      10, ntmin   =       1
<      dx0     =   0.01000, drms    =   0.00010
< SHAKE:
<      ntc     =       2, jfastw  =       0
<      tol     =   0.00001
< NMR refinement options:
<      iscale  =       0, noeskp  =       1, ipnlty  =       1, mxsub   =       1
<      scalm   = 100.00000, pencut  =   0.10000, tausw   =   0.10000
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< Cpptraj Generated Restart
<  begin time read from input coords =     0. ps
<            Begin reading energy term weight changes/NMR restraints
<  WEIGHT CHANGES:
<                          ** No weight changes given **
<  RESTRAINTS:
<  Requested file redirections:
<   LISTOUT   = POUT
<   DISANG    = DISANG-nochir-aco-hb-plan-pp-hh1.RST
<  Restraints will be read from file: DISANG-nochir-aco-hb-plan-pp-hh1.RST
< Here are comments from the DISANG input file:
< #
< #   2  RG H8        2  RG H2'        4.20    (#   )
<                        Number of restraints read =  6060
<                   Done reading weight changes/NMR restraints
<  Number of triangulated 3-point waters found:        0
<  ------------------EMAP IMAGE    1 INPUT ---------------
< map file: mmlv_rna_cut1.ccp4 is read from unit:   99
<  LX, LY, LZ              =       20      20      20
<  MODE                    =        2
<  MX, MY, MZ              =       -7      -8     -12
<  NX, NY, NZ              =       20      20      20
<  XL, YL, ZL              =   129.74  129.74  129.74
<  ALPHA,BETA,GAMMA        =    90.00   90.00   90.00
<  MAPC, MAPR, MAPS        =        1       2       3
<  MIN,MAX,MEAN,STD        =  -0.8042E+1  0.2515E+2  0.3938  0.4172E+1
<  ISPG,NSYMBT=        1       0
<  LSKFLG,NNOTE=        0      10
<  SKWMAT                  =     0.01    0.    0.
<  SKWMAT                  =     0.    0.01    0.
<  SKWMAT                  =     0.    0.    0.01
<  SKWTRN                  =     0.    0.    0.
<  EXTRA                   =     0.    0.    0.    0.    0.
<  EXTRA                   =     0.    0.    0.    0.    0.
<  EXTRA                   =     0.    0.    0.    0.    0.
<  MAPLABEL                = MAP
<  MACHST                  = DA
<  NOTES  1: bimg -v 7 -translate -25,-25,-20 -size 20,20,20 -origin 7,8,12 images/case_mmlv_
<  NOTES  2: rna1.ccp4 images/mmlv_rna_cut1.ccp4
<  DATA POINT NUMBER       =     8000
<  ----------------------- END OF EMAP IMAGE    1  --------------------------
< Rigid    1 has   4278 constrained atoms with mask: :1-132;
<     Rigid-fitting is requested for the constrained atoms with a grid:
<       x:  1 y:  1 z:  1 theta:  2 phi:  2 psi:  2
<     Atoms for Rigid    1 will be moved to fit the map
<     The constraint map is fixed in space.
< initial:    0.    0.    0.    0.    0.    0. -0.166394E+4
< result:     9.10  -20.98   12.43    0.09    1.15   -0.59 -0.278348E+4
< initial:    0.    0.    0.    0.    0.    1.57 -0.755158E+3
< result:   -38.37  -33.10   18.08    0.10    1.50    2.53 -0.268193E+4
< initial:    0.    0.    0.    0.    3.14    0. -0.382411E+3
< result:   -44.37   -0.48   18.21   -0.01    4.37   -0.80 -0.278354E+4
< initial:    0.    0.    0.    0.    3.14    1.57 -0.776370E+3
< result:     3.12   11.64   12.97    0.09    4.63    2.31 -0.268179E+4
< initial:    0.    0.    0.    3.14    0.    0. -0.382411E+3
< result:   -44.37   -0.48   18.21    3.13    1.23    0.80 -0.278354E+4
< initial:    0.    0.    0.    3.14    0.    1.57 -0.668301E+3
< result:   -44.37   -0.48   18.21    3.13    1.23    0.80 -0.278354E+4
< initial:    0.    0.    0.    3.14    3.14    0. -0.166394E+4
< result:     9.10  -20.98   12.43    3.23    4.29    0.59 -0.278348E+4
< initial:    0.    0.    0.    3.14    3.14    1.57 -0.649711E+3
< result:     9.10  -20.98   12.43    3.23    4.29    0.59 -0.278348E+4
< Rigid    1 has been fitted to: mmlv_rna_cut1.ccp4 with energy: -0.278354E+4
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1      -2.3096E+4     3.1317E+1     3.0141E+2     H3'       744
<  BOND    =      310.1207  ANGLE   =     6120.8326  DIHED      =     3096.8768
<  VDWAALS =    -1033.1005  EEL     =     2693.5210  EGB        =   -19700.7738
<  1-4 VDW =     3096.3006  1-4 EEL =   -15419.3363  RESTRAINT  =    -2260.9360
<  EMAP   =     -2783.5411  EMSCORE =  13.6072
<  EAMBER  =   -20835.5588
<  NMR restraints: Bond =  379.543   Angle =   139.034   Torsion =     4.028
< ===============================================================================
<   Maximum number of minimization cycles reached.
<                     FINAL RESULTS
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       1      -2.3096E+4     3.1317E+1     3.0141E+2     H3'       744
<  BOND    =      310.1207  ANGLE   =     6120.8326  DIHED      =     3096.8768
<  VDWAALS =    -1033.1005  EEL     =     2693.5210  EGB        =   -19700.7738
<  1-4 VDW =     3096.3006  1-4 EEL =   -15419.3363  RESTRAINT  =    -2260.9360
<  EMAP   =     -2783.5411  EMSCORE =  13.6072
<  EAMBER  =   -20835.5588
<  NMR restraints: Bond =  379.543   Angle =   139.034   Torsion =     4.028
< ===============================================================================
<  ------------------------------------------------------------------------------
<  Final Restraint Analysis for coords: emap2.x
<  Restraints, deviations, and energy contributions:    pencut =    0.10
<  ------------------------------------------------------------------------------
<      First atom        Last atom    curr. value target deviation  penalty
<  ------------------------------------------------------------------------------
<   H4'  G      2 --  H5'' G      2:    2.820    2.700    0.120    0.145 d    0: 0
<   H4'  C      3 --  H5'' C      3:    2.801    2.700    0.101    0.101 d    0: 0
<   H8   G      4 --  H3'  G      4:    3.463    3.200    0.263    0.689 d    0: 0
<   H4'  G      4 --  H5'' G      4:    2.831    2.700    0.131    0.172 d    0: 0
<   H8   G      5 --  H3'  G      5:    3.516    3.200    0.316    0.997 d    0: 0
<   H8   A      6 --  H3'  A      6:    3.757    3.200    0.557    3.072 d    0: 0
<   H2   A      6 --  H5   C      8:    5.198    5.000    0.198    0.393 d    0: 0
<   H6   C      7 --  H3'  C      7:    3.804    3.200    0.604    3.544 d    0: 0
<   H8   G     10 --  H3'  G     10:    3.467    3.200    0.267    0.711 d    0: 0
<   H4'  G     10 --  H5'' G     10:    2.801    2.700    0.101    0.102 d    0: 0
<   H2'  G     10 --  H4'  U     11:    7.379    5.000    2.379   21.290 d    0: 0
<   H3'  G     10 --  H4'  U     11:    5.661    5.000    0.661    4.112 d    0: 0
<   H2'  G     10 --  H5'  U     11:    6.522    5.000    1.522   12.715 d    0: 0
<   H3'  G     10 --  H5'  U     11:    5.511    5.000    0.511    2.611 d    0: 0
<   H3'  U     11 --  H5'' U     11:    3.980    3.300    0.680    4.301 d    0: 0
<   H4'  U     11 --  H5'  U     11:    2.905    2.700    0.205    0.422 d    0: 0
<   H8   G     12 --  H3'  G     12:    3.842    3.200    0.642    3.918 d    0: 0
<   H8   G     13 --  H3'  G     13:    3.791    3.200    0.591    3.410 d    0: 0
<   H8   G     13 --  H6   U     14:    5.118    5.000    0.118    0.139 d    0: 0
<   H6   U     14 --  H3'  U     14:    3.823    3.200    0.623    3.726 d    0: 0
<   H4'  U     14 --  H5'' U     14:    2.803    2.700    0.103    0.107 d    0: 0
<   H8   G     16 --  H2'  G     16:    4.305    4.200    0.105    0.110 d    0: 0
<   H8   G     16 --  H3'  G     16:    3.722    3.200    0.522    2.718 d    0: 0
<   H8   G     16 --  H8   A     17:    5.135    5.000    0.135    0.183 d    0: 0
<   H8   A     17 --  H3'  A     17:    3.394    3.200    0.194    0.375 d    0: 0
<   H6   C     19 --  H3'  C     19:    3.304    3.200    0.104    0.108 d    0: 0
<   H8   A     20 --  H3'  A     20:    3.698    3.200    0.498    2.484 d    0: 0
<   H2'  A     20 --  H8   G     21:    2.852    2.700    0.152    0.232 d    0: 0
<   H8   G     21 --  H3'  G     21:    3.809    3.200    0.609    3.585 d    0: 0
<   H8   A     22 --  H3'  A     22:    3.302    3.200    0.102    0.104 d    0: 0
<   H6   C     23 --  H3'  C     23:    3.547    3.200    0.347    1.207 d    0: 0
<   H8   G     26 --  H3'  G     26:    3.768    3.200    0.568    3.182 d    0: 0
<   H4'  G     26 --  H5'' G     26:    2.847    2.700    0.147    0.216 d    0: 0
<   H6   U     27 --  H3'  U     27:    3.304    3.200    0.104    0.107 d    0: 0
<   H6   U     28 --  H3'  U     28:    3.396    3.200    0.196    0.385 d    0: 0
<   H4'  U     28 --  H5'' U     28:    2.830    2.700    0.130    0.169 d    0: 0
<   H6   C     29 --  H3'  C     29:    3.547    3.200    0.347    1.208 d    0: 0
<   H8   G     30 --  H2'  G     30:    4.304    4.200    0.104    0.108 d    0: 0
<   H8   G     30 --  H3'  G     30:    3.819    3.200    0.619    3.688 d    0: 0
<   H6   C     34 --  H3'  C     34:    3.570    3.200    0.370    1.372 d    0: 0
<   H4'  C     34 --  H5'' C     34:    2.818    2.700    0.118    0.140 d    0: 0
<   H8   A     35 --  H3'  A     35:    3.685    3.200    0.485    2.354 d    0: 0
<   H4'  A     35 --  H5'' A     35:    2.806    2.700    0.106    0.112 d    0: 0
<   H6   C     36 --  H3'  C     36:    3.609    3.200    0.409    1.677 d    0: 0
<   H4'  C     36 --  H5'' C     36:    2.809    2.700    0.109    0.120 d    0: 0
<   H6   C     37 --  H3'  C     37:    3.539    3.200    0.339    1.149 d    0: 0
<   H6   C     41 --  H3'  C     41:    3.478    3.200    0.278    0.772 d    0: 0
<   H6   C     42 --  H3'  C     42:    3.425    3.200    0.225    0.508 d    0: 0
<   H4'  C     44 --  H5'' C     44:    2.825    2.700    0.125    0.156 d    0: 0
<   H4'  G     68 --  H5'' G     68:    2.811    2.700    0.111    0.124 d    0: 0
<   H4'  C     69 --  H5'' C     69:    2.805    2.700    0.105    0.110 d    0: 0
<   H8   G     70 --  H3'  G     70:    3.462    3.200    0.262    0.688 d    0: 0
<   H4'  G     70 --  H5'' G     70:    2.832    2.700    0.132    0.173 d    0: 0
<   H8   G     71 --  H3'  G     71:    3.519    3.200    0.319    1.020 d    0: 0
<   H8   A     72 --  H3'  A     72:    3.760    3.200    0.560    3.099 d    0: 0
<   H2   A     72 --  H5   C     74:    5.192    5.000    0.192    0.370 d    0: 0
<   H6   C     73 --  H3'  C     73:    3.808    3.200    0.608    3.580 d    0: 0
<   H8   G     76 --  H3'  G     76:    3.441    3.200    0.241    0.583 d    0: 0
<   H4'  G     76 --  H5'' G     76:    2.807    2.700    0.107    0.115 d    0: 0
<   H2'  G     76 --  H4'  U     77:    7.549    5.000    2.549   22.993 d    0: 0
<   H3'  G     76 --  H4'  U     77:    5.970    5.000    0.970    7.201 d    0: 0
<   H2'  G     76 --  H5'  U     77:    5.478    5.000    0.478    2.285 d    0: 0
<   H6   U     77 --  H3'  U     77:    3.459    3.200    0.259    0.672 d    0: 0
<   H3'  U     77 --  H5'' U     77:    4.012    3.300    0.712    4.616 d    0: 0
<   H4'  U     77 --  H5'  U     77:    3.088    2.700    0.388    1.504 d    0: 0
<   H8   G     78 --  H3'  G     78:    3.840    3.200    0.640    3.897 d    0: 0
<   H8   G     79 --  H3'  G     79:    3.788    3.200    0.588    3.382 d    0: 0
<   H8   G     79 --  H6   U     80:    5.105    5.000    0.105    0.110 d    0: 0
<   H6   U     80 --  H3'  U     80:    3.801    3.200    0.601    3.511 d    0: 0
<   H4'  U     80 --  H5'' U     80:    2.810    2.700    0.110    0.120 d    0: 0
<   H8   G     82 --  H2'  G     82:    4.302    4.200    0.102    0.105 d    0: 0
<   H8   G     82 --  H3'  G     82:    3.722    3.200    0.522    2.719 d    0: 0
<   H8   G     82 --  H8   A     83:    5.127    5.000    0.127    0.161 d    0: 0
<   H8   A     83 --  H3'  A     83:    3.409    3.200    0.209    0.438 d    0: 0
<   H6   C     85 --  H3'  C     85:    3.369    3.200    0.169    0.286 d    0: 0
<   H8   A     86 --  H3'  A     86:    3.763    3.200    0.563    3.134 d    0: 0
<   H2'  A     86 --  H8   G     87:    2.858    2.700    0.158    0.251 d    0: 0
<   H8   G     87 --  H3'  G     87:    3.769    3.200    0.569    3.192 d    0: 0
<   H8   A     88 --  H3'  A     88:    3.517    3.200    0.317    1.002 d    0: 0
<   H6   C     89 --  H3'  C     89:    3.564    3.200    0.364    1.328 d    0: 0
<   H8   G     90 --  H3'  G     90:    3.554    3.200    0.354    1.255 d    0: 0
<   H8   G     92 --  H3'  G     92:    3.772    3.200    0.572    3.225 d    0: 0
<   H4'  G     92 --  H5'' G     92:    2.851    2.700    0.151    0.227 d    0: 0
<   H6   U     93 --  H3'  U     93:    3.333    3.200    0.133    0.177 d    0: 0
<   H6   U     94 --  H3'  U     94:    3.409    3.200    0.209    0.438 d    0: 0
<   H4'  U     94 --  H5'' U     94:    2.828    2.700    0.128    0.164 d    0: 0
<   H6   C     95 --  H3'  C     95:    3.571    3.200    0.371    1.380 d    0: 0
<   H8   G     96 --  H2'  G     96:    4.306    4.200    0.106    0.111 d    0: 0
<   H8   G     96 --  H3'  G     96:    3.819    3.200    0.619    3.691 d    0: 0
<   H6   C    100 --  H3'  C    100:    3.571    3.200    0.371    1.375 d    0: 0
<   H4'  C    100 --  H5'' C    100:    2.819    2.700    0.119    0.141 d    0: 0
<   H8   A    101 --  H3'  A    101:    3.672    3.200    0.472    2.224 d    0: 0
<   H4'  A    101 --  H5'' A    101:    2.806    2.700    0.106    0.111 d    0: 0
<   H6   C    102 --  H3'  C    102:    3.612    3.200    0.412    1.694 d    0: 0
<   H4'  C    102 --  H5'' C    102:    2.808    2.700    0.108    0.116 d    0: 0
<   H6   C    103 --  H3'  C    103:    3.539    3.200    0.339    1.152 d    0: 0
<   H6   C    107 --  H3'  C    107:    3.496    3.200    0.296    0.875 d    0: 0
<   H6   C    108 --  H3'  C    108:    3.422    3.200    0.222    0.494 d    0: 0
<   H4'  C    110 --  H5'' C    110:    2.818    2.700    0.118    0.140 d    0: 0
<   H6   C     47 --  H3'  C     47:    3.570    3.000    0.570    3.203 d    0: 0
<   H4'  C     47 --  H5'' C     47:    2.821    2.700    0.121    0.147 d    0: 0
<   H6   C     48 --  H3'  C     48:    3.597    3.000    0.597    3.474 d    0: 0
<   H6   C     49 --  H3'  C     49:    3.512    3.000    0.512    2.618 d    0: 0
<   H6   U     50 --  H3'  U     50:    3.528    3.000    0.528    2.777 d    0: 0
<   H4'  U     50 --  H5'' U     50:    2.820    2.700    0.120    0.145 d    0: 0
<   H8   G     51 --  H2'  G     51:    4.104    4.000    0.104    0.108 d    0: 0
<   H8   G     51 --  H3'  G     51:    3.585    3.000    0.585    3.353 d    0: 0
<   H8   G     52 --  H3'  G     52:    3.582    3.000    0.582    3.321 d    0: 0
<   H8   G     53 --  H3'  G     53:    3.258    3.000    0.258    0.664 d    0: 0
<   H8   A     54 --  H3'  A     54:    3.112    3.000    0.112    0.126 d    0: 0
<   H8   G     55 --  H3'  G     55:    3.395    3.200    0.195    0.379 d    0: 0
<   H4'  G     55 --  H5'' G     55:    2.828    2.700    0.128    0.163 d    0: 0
<   H8   A     56 --  H3'  A     56:    3.862    3.200    0.662    4.119 d    0: 0
<   H6   C     57 --  H3'  C     57:    3.551    3.200    0.351    1.235 d    0: 0
<   H4'  C     57 --  H5'  C     57:    2.855    2.700    0.155    0.240 d    0: 0
<   H4'  C     57 --  H5'' C     57:    2.978    2.700    0.278    0.770 d    0: 0
<   H8   G     58 --  H3'  G     58:    3.802    3.200    0.602    3.524 d    0: 0
<   H4'  G     58 --  H5'' G     58:    3.087    2.700    0.387    1.496 d    0: 0
<   H6   U     59 --  H3'  U     59:    3.258    3.000    0.258    0.668 d    0: 0
<   H4'  U     59 --  H5'' U     59:    2.842    2.700    0.142    0.202 d    0: 0
<   H6   C     60 --  H3'  C     60:    3.472    3.000    0.472    2.225 d    0: 0
<   H4'  C     60 --  H5'' C     60:    2.834    2.700    0.134    0.180 d    0: 0
<   H6   C     61 --  H3'  C     61:    3.612    3.000    0.612    3.622 d    0: 0
<   H4'  C     61 --  H5'' C     61:    2.820    2.700    0.120    0.143 d    0: 0
<   H6   C     62 --  H3'  C     62:    3.530    3.000    0.530    2.805 d    0: 0
<   H4'  C     62 --  H5'' C     62:    2.820    2.700    0.120    0.145 d    0: 0
<   H8   A     63 --  H3'  A     63:    3.538    3.000    0.538    2.879 d    0: 0
<   H4'  A     63 --  H5'' A     63:    2.816    2.700    0.116    0.134 d    0: 0
<   H8   G     64 --  H2'  G     64:    4.104    4.000    0.104    0.109 d    0: 0
<   H8   G     64 --  H3'  G     64:    3.601    3.000    0.601    3.512 d    0: 0
<   H8   G     65 --  H3'  G     65:    3.605    3.000    0.605    3.552 d    0: 0
<   H8   G3    66 --  H3'  G3    66:    3.225    3.000    0.225    0.508 d    0: 0
<   H6   C    113 --  H3'  C    113:    3.559    3.000    0.559    3.094 d    0: 0
<   H4'  C    113 --  H5'' C    113:    2.829    2.700    0.129    0.167 d    0: 0
<   H6   C    114 --  H3'  C    114:    3.560    3.000    0.560    3.104 d    0: 0
<   H6   C    115 --  H3'  C    115:    3.464    3.000    0.464    2.149 d    0: 0
<   H6   U    116 --  H3'  U    116:    3.522    3.000    0.522    2.724 d    0: 0
<   H4'  U    116 --  H5'' U    116:    2.819    2.700    0.119    0.142 d    0: 0
<   H8   G    117 --  H2'  G    117:    4.103    4.000    0.103    0.106 d    0: 0
<   H8   G    117 --  H3'  G    117:    3.590    3.000    0.590    3.396 d    0: 0
<   H8   G    118 --  H3'  G    118:    3.596    3.000    0.596    3.458 d    0: 0
<   H8   G    119 --  H3'  G    119:    3.283    3.000    0.283    0.804 d    0: 0
<   H8   A    120 --  H3'  A    120:    3.181    3.000    0.181    0.327 d    0: 0
<   H8   G    121 --  H3'  G    121:    3.360    3.200    0.160    0.256 d    0: 0
<   H4'  G    121 --  H5'' G    121:    2.836    2.700    0.136    0.186 d    0: 0
<   H8   A    122 --  H3'  A    122:    3.860    3.200    0.660    4.099 d    0: 0
<   H3'  A    122 --  H5'' A    122:    3.404    3.300    0.104    0.109 d    0: 0
<   H6   C    123 --  H3'  C    123:    3.700    3.200    0.500    2.502 d    0: 0
<   H4'  C    123 --  H5'' C    123:    3.007    2.700    0.307    0.943 d    0: 0
<   H8   G    124 --  H3'  G    124:    3.802    3.200    0.602    3.516 d    0: 0
<   H4'  G    124 --  H5'' G    124:    3.052    2.700    0.352    1.239 d    0: 0
<   H6   U    125 --  H3'  U    125:    3.385    3.000    0.385    1.479 d    0: 0
<   H4'  U    125 --  H5'' U    125:    2.836    2.700    0.136    0.186 d    0: 0
<   H6   C    126 --  H3'  C    126:    3.498    3.000    0.498    2.478 d    0: 0
<   H4'  C    126 --  H5'' C    126:    2.828    2.700    0.128    0.164 d    0: 0
<   H6   C    127 --  H2'  C    127:    4.101    4.000    0.101    0.102 d    0: 0
<   H6   C    127 --  H3'  C    127:    3.618    3.000    0.618    3.682 d    0: 0
<   H4'  C    127 --  H5'' C    127:    2.819    2.700    0.119    0.142 d    0: 0
<   H6   C    128 --  H3'  C    128:    3.509    3.000    0.509    2.585 d    0: 0
<   H4'  C    128 --  H5'' C    128:    2.824    2.700    0.124    0.153 d    0: 0
<   H8   A    129 --  H2'  A    129:    4.100    4.000    0.100    0.101 d    0: 0
<   H8   A    129 --  H3'  A    129:    3.528    3.000    0.528    2.783 d    0: 0
<   H4'  A    129 --  H5'' A    129:    2.815    2.700    0.115    0.133 d    0: 0
<   H8   G    130 --  H3'  G    130:    3.587    3.000    0.587    3.368 d    0: 0
<   H8   G    131 --  H3'  G    131:    3.594    3.000    0.594    3.439 d    0: 0
<   H8   G3   132 --  H3'  G3   132:    3.185    3.000    0.185    0.343 d    0: 0
<   H8   A     22 --  N1   C    126:    7.272    5.000    2.272   20.217 d    0: 0
<   H2   A     22 --  N1   C    126:    6.229    5.000    1.229    9.787 d    0: 0
<   H8   A    122 --  C1'  G     26:    5.219    5.000    0.219    0.480 d    0: 0
<   H2   A    122 --  C1'  G     26:    5.674    5.000    0.674    4.243 d    0: 0
<   H2   A    122 --  C4'  G     26:    5.269    5.000    0.269    0.721 d    0: 0
<   H8   A     88 --  C1'  C     60:    6.096    5.000    1.096    8.463 d    0: 0
<   H2   A     88 --  C1'  C     60:    5.187    5.000    0.187    0.351 d    0: 0
<   H8   A     56 --  N9   G     92:    6.402    5.000    1.402   11.522 d    0: 0
<   H2   A     56 --  N9   G     92:    6.576    5.000    1.576   13.260 d    0: 0
<   H8   A     45 --  H3'  A     45:    3.561    3.000    0.561    3.106 d    0: 0
<   H4'  A     45 --  H5'' A     45:    2.875    2.700    0.175    0.305 d    0: 0
<   H8   A     46 --  H2'  A     46:    4.103    4.000    0.103    0.107 d    0: 0
<   H8   A     46 --  H3'  A     46:    3.545    3.000    0.545    2.950 d    0: 0
<   H8   A    111 --  H3'  A    111:    3.564    3.000    0.564    3.143 d    0: 0
<   H4'  A    111 --  H5'' A    111:    2.844    2.700    0.144    0.208 d    0: 0
<   H8   A    112 --  H3'  A    112:    3.551    3.000    0.551    3.013 d    0: 0
<   C1'  G5     1 --  O2'  G5     1:  115.496  109.000    6.496    0.129 a
<   C1'  G      2 --  O2'  G      2:  115.310  109.000    6.310    0.121 a
<   C1'  C      3 --  O2'  C      3:  115.452  109.000    6.452    0.127 a
<   C1'  G      4 --  O2'  G      4:  115.516  109.000    6.516    0.129 a
<   C1'  G      5 --  O2'  G      5:  115.369  109.000    6.369    0.124 a
<   C1'  A      6 --  O2'  A      6:  115.376  109.000    6.376    0.124 a
<   C1'  C      7 --  O2'  C      7:  115.342  109.000    6.342    0.123 a
<   C1'  C      8 --  O2'  C      8:  115.346  109.000    6.346    0.123 a
<   C1'  C      9 --  O2'  C      9:  115.386  109.000    6.386    0.124 a
<   C1'  G     10 --  O2'  G     10:  115.494  109.000    6.494    0.128 a
<   C1'  U     11 --  O2'  U     11:  115.464  109.000    6.464    0.127 a
<   C1'  G     12 --  O2'  G     12:  115.539  109.000    6.539    0.130 a
<   C1'  G     13 --  O2'  G     13:  115.324  109.000    6.324    0.122 a
<   C1'  U     14 --  O2'  U     14:  115.575  109.000    6.575    0.132 a
<   C1'  G     15 --  O2'  G     15:  115.316  109.000    6.316    0.121 a
<   C1'  G     16 --  O2'  G     16:  115.412  109.000    6.412    0.125 a
<   C1'  A     17 --  O2'  A     17:  115.373  109.000    6.373    0.124 a
<   C1'  A     18 --  O2'  A     18:  115.398  109.000    6.398    0.125 a
<   C1'  C     19 --  O2'  C     19:  115.412  109.000    6.412    0.125 a
<   C1'  A     20 --  O2'  A     20:  115.432  109.000    6.432    0.126 a
<   C1'  G     21 --  O2'  G     21:  115.397  109.000    6.397    0.125 a
<   C1'  A     22 --  O2'  A     22:  115.504  109.000    6.504    0.129 a
<   C1'  C     23 --  O2'  C     23:  115.485  109.000    6.485    0.128 a
<   C1'  G     24 --  O2'  G     24:  115.423  109.000    6.423    0.126 a
<   C1'  U     25 --  O2'  U     25:  115.477  109.000    6.477    0.128 a
<   C1'  G     26 --  O2'  G     26:  115.390  109.000    6.390    0.124 a
<   C1'  U     27 --  O2'  U     27:  115.307  109.000    6.307    0.121 a
<   C1'  U     28 --  O2'  U     28:  115.427  109.000    6.427    0.126 a
<   C1'  C     29 --  O2'  C     29:  115.380  109.000    6.380    0.124 a
<   C1'  G     30 --  O2'  G     30:  115.412  109.000    6.412    0.125 a
<   C1'  G     31 --  O2'  G     31:  115.518  109.000    6.518    0.129 a
<   C1'  A     32 --  O2'  A     32:  115.499  109.000    6.499    0.129 a
<   C1'  A     33 --  O2'  A     33:  115.429  109.000    6.429    0.126 a
<   C1'  C     34 --  O2'  C     34:  115.458  109.000    6.458    0.127 a
<   C1'  A     35 --  O2'  A     35:  115.464  109.000    6.464    0.127 a
<   C1'  C     36 --  O2'  C     36:  115.406  109.000    6.406    0.125 a
<   C1'  C     37 --  O2'  C     37:  115.490  109.000    6.490    0.128 a
<   C1'  C     38 --  O2'  C     38:  115.439  109.000    6.439    0.126 a
<   C1'  G     39 --  O2'  G     39:  115.417  109.000    6.417    0.125 a
<   C1'  G     40 --  O2'  G     40:  115.354  109.000    6.354    0.123 a
<   C1'  C     41 --  O2'  C     41:  115.466  109.000    6.466    0.127 a
<   C1'  C     42 --  O2'  C     42:  115.522  109.000    6.522    0.130 a
<   C1'  G     43 --  O2'  G     43:  115.429  109.000    6.429    0.126 a
<   C1'  C     44 --  O2'  C     44:  115.408  109.000    6.408    0.125 a
<   C1'  A     45 --  O2'  A     45:  115.440  109.000    6.440    0.126 a
<   C1'  A     46 --  O2'  A     46:  115.466  109.000    6.466    0.127 a
<   C1'  C     47 --  O2'  C     47:  115.370  109.000    6.370    0.124 a
<   C1'  C     48 --  O2'  C     48:  115.429  109.000    6.429    0.126 a
<   C1'  C     49 --  O2'  C     49:  115.335  109.000    6.335    0.122 a
<   C1'  U     50 --  O2'  U     50:  115.398  109.000    6.398    0.125 a
<   C1'  G     51 --  O2'  G     51:  115.485  109.000    6.485    0.128 a
<   C1'  G     52 --  O2'  G     52:  115.518  109.000    6.518    0.129 a
<   C1'  G     53 --  O2'  G     53:  115.403  109.000    6.403    0.125 a
<   C1'  A     54 --  O2'  A     54:  115.514  109.000    6.514    0.129 a
<   C1'  G     55 --  O2'  G     55:  115.357  109.000    6.357    0.123 a
<   C1'  A     56 --  O2'  A     56:  115.548  109.000    6.548    0.131 a
<   C1'  C     57 --  O2'  C     57:  115.413  109.000    6.413    0.125 a
<   C1'  G     58 --  O2'  G     58:  115.535  109.000    6.535    0.130 a
<   C1'  U     59 --  O2'  U     59:  115.458  109.000    6.458    0.127 a
<   C1'  C     60 --  O2'  C     60:  115.416  109.000    6.416    0.125 a
<   C1'  C     61 --  O2'  C     61:  115.374  109.000    6.374    0.124 a
<   C1'  C     62 --  O2'  C     62:  115.411  109.000    6.411    0.125 a
<   C1'  A     63 --  O2'  A     63:  115.403  109.000    6.403    0.125 a
<   C1'  G     64 --  O2'  G     64:  115.436  109.000    6.436    0.126 a
<   C1'  G     65 --  O2'  G     65:  115.436  109.000    6.436    0.126 a
<   C1'  G3    66 --  O2'  G3    66:  115.516  109.000    6.516    0.129 a
<   C1'  G5    67 --  O2'  G5    67:  115.419  109.000    6.419    0.126 a
<   C1'  G     68 --  O2'  G     68:  115.401  109.000    6.401    0.125 a
<   C1'  C     69 --  O2'  C     69:  115.416  109.000    6.416    0.125 a
<   C1'  G     70 --  O2'  G     70:  115.474  109.000    6.474    0.128 a
<   C1'  G     71 --  O2'  G     71:  115.475  109.000    6.475    0.128 a
<   C1'  A     72 --  O2'  A     72:  115.388  109.000    6.388    0.124 a
<   C1'  C     73 --  O2'  C     73:  115.427  109.000    6.427    0.126 a
<   C1'  C     74 --  O2'  C     74:  115.393  109.000    6.393    0.124 a
<   C1'  C     75 --  O2'  C     75:  115.513  109.000    6.513    0.129 a
<   C1'  G     76 --  O2'  G     76:  115.392  109.000    6.392    0.124 a
<   C1'  U     77 --  O2'  U     77:  115.442  109.000    6.442    0.126 a
<   C1'  G     78 --  O2'  G     78:  115.443  109.000    6.443    0.126 a
<   C1'  G     79 --  O2'  G     79:  115.464  109.000    6.464    0.127 a
<   C1'  U     80 --  O2'  U     80:  115.447  109.000    6.447    0.127 a
<   C1'  G     81 --  O2'  G     81:  115.440  109.000    6.440    0.126 a
<   C1'  G     82 --  O2'  G     82:  115.471  109.000    6.471    0.128 a
<   C1'  A     83 --  O2'  A     83:  115.467  109.000    6.467    0.127 a
<   C1'  A     84 --  O2'  A     84:  115.430  109.000    6.430    0.126 a
<   C1'  C     85 --  O2'  C     85:  115.480  109.000    6.480    0.128 a
<   C1'  A     86 --  O2'  A     86:  115.385  109.000    6.385    0.124 a
<   C1'  G     87 --  O2'  G     87:  115.467  109.000    6.467    0.127 a
<   C1'  A     88 --  O2'  A     88:  115.363  109.000    6.363    0.123 a
<   C1'  C     89 --  O2'  C     89:  115.312  109.000    6.312    0.121 a
<   C1'  G     90 --  O2'  G     90:  115.446  109.000    6.446    0.127 a
<   C1'  U     91 --  O2'  U     91:  115.527  109.000    6.527    0.130 a
<   C1'  G     92 --  O2'  G     92:  115.427  109.000    6.427    0.126 a
<   C1'  U     93 --  O2'  U     93:  115.482  109.000    6.482    0.128 a
<   C1'  U     94 --  O2'  U     94:  115.511  109.000    6.511    0.129 a
<   C1'  C     95 --  O2'  C     95:  115.462  109.000    6.462    0.127 a
<   C1'  G     96 --  O2'  G     96:  115.449  109.000    6.449    0.127 a
<   C1'  G     97 --  O2'  G     97:  115.415  109.000    6.415    0.125 a
<   C1'  A     98 --  O2'  A     98:  115.447  109.000    6.447    0.127 a
<   C1'  A     99 --  O2'  A     99:  115.399  109.000    6.399    0.125 a
<   C1'  C    100 --  O2'  C    100:  115.386  109.000    6.386    0.124 a
<   C1'  A    101 --  O2'  A    101:  115.445  109.000    6.445    0.127 a
<   C1'  C    102 --  O2'  C    102:  115.477  109.000    6.477    0.128 a
<   C1'  C    103 --  O2'  C    103:  115.479  109.000    6.479    0.128 a
<   C1'  C    104 --  O2'  C    104:  115.369  109.000    6.369    0.124 a
<   C1'  G    105 --  O2'  G    105:  115.464  109.000    6.464    0.127 a
<   C1'  G    106 --  O2'  G    106:  115.437  109.000    6.437    0.126 a
<   C1'  C    107 --  O2'  C    107:  115.434  109.000    6.434    0.126 a
<   C1'  C    108 --  O2'  C    108:  115.418  109.000    6.418    0.125 a
<   C1'  G    109 --  O2'  G    109:  115.425  109.000    6.425    0.126 a
<   C1'  C    110 --  O2'  C    110:  115.477  109.000    6.477    0.128 a
<   C1'  A    111 --  O2'  A    111:  115.503  109.000    6.503    0.129 a
<   C1'  A    112 --  O2'  A    112:  115.453  109.000    6.453    0.127 a
<   C1'  C    113 --  O2'  C    113:  115.513  109.000    6.513    0.129 a
<   C1'  C    114 --  O2'  C    114:  115.434  109.000    6.434    0.126 a
<   C1'  C    115 --  O2'  C    115:  115.445  109.000    6.445    0.127 a
<   C1'  U    116 --  O2'  U    116:  115.456  109.000    6.456    0.127 a
<   C1'  G    117 --  O2'  G    117:  115.381  109.000    6.381    0.124 a
<   C1'  G    118 --  O2'  G    118:  115.558  109.000    6.558    0.131 a
<   C1'  G    119 --  O2'  G    119:  115.411  109.000    6.411    0.125 a
<   C1'  A    120 --  O2'  A    120:  115.440  109.000    6.440    0.126 a
<   C1'  G    121 --  O2'  G    121:  115.492  109.000    6.492    0.128 a
<   C1'  A    122 --  O2'  A    122:  115.448  109.000    6.448    0.127 a
<   C1'  C    123 --  O2'  C    123:  115.326  109.000    6.326    0.122 a
<   C1'  G    124 --  O2'  G    124:  115.481  109.000    6.481    0.128 a
<   C1'  U    125 --  O2'  U    125:  115.447  109.000    6.447    0.127 a
<   C1'  C    126 --  O2'  C    126:  115.421  109.000    6.421    0.126 a
<   C1'  C    127 --  O2'  C    127:  115.418  109.000    6.418    0.125 a
<   C1'  C    128 --  O2'  C    128:  115.468  109.000    6.468    0.127 a
<   C1'  A    129 --  O2'  A    129:  115.532  109.000    6.532    0.130 a
<   C1'  G    130 --  O2'  G    130:  115.508  109.000    6.508    0.129 a
<   C1'  G    131 --  O2'  G    131:  115.359  109.000    6.359    0.123 a
<   C1'  G3   132 --  O2'  G3   132:  115.293  109.000    6.293    0.121 a
<   C3'  G5     1 --  O2'  G5     1:  102.827  109.500    6.673    0.136 a
<   C3'  G      2 --  O2'  G      2:  102.682  109.500    6.818    0.142 a
<   C3'  C      3 --  O2'  C      3:  102.714  109.500    6.786    0.140 a
<   C3'  G      4 --  O2'  G      4:  102.656  109.500    6.844    0.143 a
<   C3'  G      5 --  O2'  G      5:  102.652  109.500    6.848    0.143 a
<   C3'  A      6 --  O2'  A      6:  102.639  109.500    6.861    0.143 a
<   C3'  C      7 --  O2'  C      7:  102.782  109.500    6.718    0.137 a
<   C3'  C      8 --  O2'  C      8:  102.750  109.500    6.750    0.139 a
<   C3'  C      9 --  O2'  C      9:  102.704  109.500    6.796    0.141 a
<   C3'  G     10 --  O2'  G     10:  102.609  109.500    6.891    0.145 a
<   C3'  U     11 --  O2'  U     11:  102.654  109.500    6.846    0.143 a
<   C3'  G     12 --  O2'  G     12:  102.704  109.500    6.796    0.141 a
<   C3'  G     13 --  O2'  G     13:  102.666  109.500    6.834    0.142 a
<   C3'  U     14 --  O2'  U     14:  102.668  109.500    6.832    0.142 a
<   C3'  G     15 --  O2'  G     15:  102.687  109.500    6.813    0.141 a
<   C3'  G     16 --  O2'  G     16:  102.645  109.500    6.855    0.143 a
<   C3'  A     17 --  O2'  A     17:  102.702  109.500    6.798    0.141 a
<   C3'  A     18 --  O2'  A     18:  102.732  109.500    6.768    0.140 a
<   C3'  C     19 --  O2'  C     19:  102.692  109.500    6.808    0.141 a
<   C3'  A     20 --  O2'  A     20:  102.677  109.500    6.823    0.142 a
<   C3'  G     21 --  O2'  G     21:  102.749  109.500    6.751    0.139 a
<   C3'  A     22 --  O2'  A     22:  102.733  109.500    6.767    0.140 a
<   C3'  C     23 --  O2'  C     23:  102.768  109.500    6.732    0.138 a
<   C3'  G     24 --  O2'  G     24:  102.665  109.500    6.835    0.142 a
<   C3'  U     25 --  O2'  U     25:  102.643  109.500    6.857    0.143 a
<   C3'  G     26 --  O2'  G     26:  102.617  109.500    6.883    0.144 a
<   C3'  U     27 --  O2'  U     27:  102.754  109.500    6.746    0.139 a
<   C3'  U     28 --  O2'  U     28:  102.659  109.500    6.841    0.143 a
<   C3'  C     29 --  O2'  C     29:  102.820  109.500    6.680    0.136 a
<   C3'  G     30 --  O2'  G     30:  102.687  109.500    6.813    0.141 a
<   C3'  G     31 --  O2'  G     31:  102.611  109.500    6.889    0.145 a
<   C3'  A     32 --  O2'  A     32:  102.611  109.500    6.889    0.145 a
<   C3'  A     33 --  O2'  A     33:  102.661  109.500    6.839    0.142 a
<   C3'  C     34 --  O2'  C     34:  102.787  109.500    6.713    0.137 a
<   C3'  A     35 --  O2'  A     35:  102.720  109.500    6.780    0.140 a
<   C3'  C     36 --  O2'  C     36:  102.716  109.500    6.784    0.140 a
<   C3'  C     37 --  O2'  C     37:  102.705  109.500    6.795    0.141 a
<   C3'  C     38 --  O2'  C     38:  102.757  109.500    6.743    0.138 a
<   C3'  G     39 --  O2'  G     39:  102.598  109.500    6.902    0.145 a
<   C3'  G     40 --  O2'  G     40:  102.686  109.500    6.814    0.141 a
<   C3'  C     41 --  O2'  C     41:  102.622  109.500    6.878    0.144 a
<   C3'  C     42 --  O2'  C     42:  102.684  109.500    6.816    0.142 a
<   C3'  G     43 --  O2'  G     43:  102.677  109.500    6.823    0.142 a
<   C3'  C     44 --  O2'  C     44:  102.729  109.500    6.771    0.140 a
<   C3'  A     45 --  O2'  A     45:  102.735  109.500    6.765    0.139 a
<   C3'  A     46 --  O2'  A     46:  102.634  109.500    6.866    0.144 a
<   C3'  C     47 --  O2'  C     47:  102.743  109.500    6.757    0.139 a
<   C3'  C     48 --  O2'  C     48:  102.785  109.500    6.715    0.137 a
<   C3'  C     49 --  O2'  C     49:  102.765  109.500    6.735    0.138 a
<   C3'  U     50 --  O2'  U     50:  102.791  109.500    6.709    0.137 a
<   C3'  G     51 --  O2'  G     51:  102.657  109.500    6.843    0.143 a
<   C3'  G     52 --  O2'  G     52:  102.682  109.500    6.818    0.142 a
<   C3'  G     53 --  O2'  G     53:  102.684  109.500    6.816    0.142 a
<   C3'  A     54 --  O2'  A     54:  102.653  109.500    6.847    0.143 a
<   C3'  G     55 --  O2'  G     55:  102.670  109.500    6.830    0.142 a
<   C3'  A     56 --  O2'  A     56:  102.661  109.500    6.839    0.142 a
<   C3'  C     57 --  O2'  C     57:  102.650  109.500    6.850    0.143 a
<   C3'  G     58 --  O2'  G     58:  102.721  109.500    6.779    0.140 a
<   C3'  U     59 --  O2'  U     59:  102.689  109.500    6.811    0.141 a
<   C3'  C     60 --  O2'  C     60:  102.693  109.500    6.807    0.141 a
<   C3'  C     61 --  O2'  C     61:  102.659  109.500    6.841    0.143 a
<   C3'  C     62 --  O2'  C     62:  102.666  109.500    6.834    0.142 a
<   C3'  A     63 --  O2'  A     63:  102.781  109.500    6.719    0.138 a
<   C3'  G     64 --  O2'  G     64:  102.687  109.500    6.813    0.141 a
<   C3'  G     65 --  O2'  G     65:  102.757  109.500    6.743    0.139 a
<   C3'  G3    66 --  O2'  G3    66:  102.598  109.500    6.902    0.145 a
<   C3'  G5    67 --  O2'  G5    67:  102.703  109.500    6.797    0.141 a
<   C3'  G     68 --  O2'  G     68:  102.617  109.500    6.883    0.144 a
<   C3'  C     69 --  O2'  C     69:  102.735  109.500    6.765    0.139 a
<   C3'  G     70 --  O2'  G     70:  102.791  109.500    6.709    0.137 a
<   C3'  G     71 --  O2'  G     71:  102.655  109.500    6.845    0.143 a
<   C3'  A     72 --  O2'  A     72:  102.702  109.500    6.798    0.141 a
<   C3'  C     73 --  O2'  C     73:  102.727  109.500    6.773    0.140 a
<   C3'  C     74 --  O2'  C     74:  102.676  109.500    6.824    0.142 a
<   C3'  C     75 --  O2'  C     75:  102.790  109.500    6.710    0.137 a
<   C3'  G     76 --  O2'  G     76:  102.688  109.500    6.812    0.141 a
<   C3'  U     77 --  O2'  U     77:  102.578  109.500    6.922    0.146 a
<   C3'  G     78 --  O2'  G     78:  102.713  109.500    6.787    0.140 a
<   C3'  G     79 --  O2'  G     79:  102.496  109.500    7.004    0.149 a
<   C3'  U     80 --  O2'  U     80:  102.765  109.500    6.735    0.138 a
<   C3'  G     81 --  O2'  G     81:  102.680  109.500    6.820    0.142 a
<   C3'  G     82 --  O2'  G     82:  102.781  109.500    6.719    0.138 a
<   C3'  A     83 --  O2'  A     83:  102.723  109.500    6.777    0.140 a
<   C3'  A     84 --  O2'  A     84:  102.700  109.500    6.800    0.141 a
<   C3'  C     85 --  O2'  C     85:  102.702  109.500    6.798    0.141 a
<   C3'  A     86 --  O2'  A     86:  102.656  109.500    6.844    0.143 a
<   C3'  G     87 --  O2'  G     87:  102.743  109.500    6.757    0.139 a
<   C3'  A     88 --  O2'  A     88:  102.747  109.500    6.753    0.139 a
<   C3'  C     89 --  O2'  C     89:  102.690  109.500    6.810    0.141 a
<   C3'  G     90 --  O2'  G     90:  102.685  109.500    6.815    0.141 a
<   C3'  U     91 --  O2'  U     91:  102.705  109.500    6.795    0.141 a
<   C3'  G     92 --  O2'  G     92:  102.629  109.500    6.871    0.144 a
<   C3'  U     93 --  O2'  U     93:  102.613  109.500    6.887    0.144 a
<   C3'  U     94 --  O2'  U     94:  102.694  109.500    6.806    0.141 a
<   C3'  C     95 --  O2'  C     95:  102.621  109.500    6.879    0.144 a
<   C3'  G     96 --  O2'  G     96:  102.684  109.500    6.816    0.142 a
<   C3'  G     97 --  O2'  G     97:  102.649  109.500    6.851    0.143 a
<   C3'  A     98 --  O2'  A     98:  102.741  109.500    6.759    0.139 a
<   C3'  A     99 --  O2'  A     99:  102.724  109.500    6.776    0.140 a
<   C3'  C    100 --  O2'  C    100:  102.675  109.500    6.825    0.142 a
<   C3'  A    101 --  O2'  A    101:  102.730  109.500    6.770    0.140 a
<   C3'  C    102 --  O2'  C    102:  102.633  109.500    6.867    0.144 a
<   C3'  C    103 --  O2'  C    103:  102.674  109.500    6.826    0.142 a
<   C3'  C    104 --  O2'  C    104:  102.715  109.500    6.785    0.140 a
<   C3'  G    105 --  O2'  G    105:  102.754  109.500    6.746    0.139 a
<   C3'  G    106 --  O2'  G    106:  102.656  109.500    6.844    0.143 a
<   C3'  C    107 --  O2'  C    107:  102.637  109.500    6.863    0.143 a
<   C3'  C    108 --  O2'  C    108:  102.636  109.500    6.864    0.144 a
<   C3'  G    109 --  O2'  G    109:  102.687  109.500    6.813    0.141 a
<   C3'  C    110 --  O2'  C    110:  102.725  109.500    6.775    0.140 a
<   C3'  A    111 --  O2'  A    111:  102.663  109.500    6.837    0.142 a
<   C3'  A    112 --  O2'  A    112:  102.707  109.500    6.793    0.141 a
<   C3'  C    113 --  O2'  C    113:  102.737  109.500    6.763    0.139 a
<   C3'  C    114 --  O2'  C    114:  102.741  109.500    6.759    0.139 a
<   C3'  C    115 --  O2'  C    115:  102.675  109.500    6.825    0.142 a
<   C3'  U    116 --  O2'  U    116:  102.785  109.500    6.715    0.137 a
<   C3'  G    117 --  O2'  G    117:  102.772  109.500    6.728    0.138 a
<   C3'  G    118 --  O2'  G    118:  102.638  109.500    6.862    0.143 a
<   C3'  G    119 --  O2'  G    119:  102.626  109.500    6.874    0.144 a
<   C3'  A    120 --  O2'  A    120:  102.789  109.500    6.711    0.137 a
<   C3'  G    121 --  O2'  G    121:  102.688  109.500    6.812    0.141 a
<   C3'  A    122 --  O2'  A    122:  102.776  109.500    6.724    0.138 a
<   C3'  C    123 --  O2'  C    123:  102.686  109.500    6.814    0.141 a
<   C3'  G    124 --  O2'  G    124:  102.746  109.500    6.754    0.139 a
<   C3'  U    125 --  O2'  U    125:  102.675  109.500    6.825    0.142 a
<   C3'  C    126 --  O2'  C    126:  102.679  109.500    6.821    0.142 a
<   C3'  C    127 --  O2'  C    127:  102.597  109.500    6.903    0.145 a
<   C3'  C    128 --  O2'  C    128:  102.678  109.500    6.822    0.142 a
<   C3'  A    129 --  O2'  A    129:  102.679  109.500    6.821    0.142 a
<   C3'  G    130 --  O2'  G    130:  102.728  109.500    6.772    0.140 a
<   C3'  G    131 --  O2'  G    131:  102.629  109.500    6.871    0.144 a
<   C3'  G3   132 --  O2'  G3   132:  102.726  109.500    6.774    0.140 a
<   C3'  G5     1 --  O4'  G5     1:   95.231  105.500   10.269    0.321 a
<   C3'  G      2 --  O4'  G      2:   98.041  105.500    7.459    0.169 a
<   C3'  C      3 --  O4'  C      3:   93.736  105.500   11.764    0.412 a
<   C3'  G      4 --  O4'  G      4:   94.359  105.500   11.141    0.374 a
<   C3'  G      5 --  O4'  G      5:   95.029  105.500   10.471    0.333 a
<   C3'  A      6 --  O4'  A      6:   93.404  105.500   12.096    0.432 a
<   C3'  C      7 --  O4'  C      7:   97.435  105.500    8.065    0.198 a
<   C3'  C      8 --  O4'  C      8:   96.898  105.500    8.602    0.225 a
<   C3'  C      9 --  O4'  C      9:   94.268  105.500   11.232    0.380 a
<   C3'  G     10 --  O4'  G     10:   95.908  105.500    9.592    0.280 a
<   C3'  U     11 --  O4'  U     11:   90.942  105.500   14.558    0.582 a
<   C3'  G     12 --  O4'  G     12:   96.763  105.500    8.737    0.233 a
<   C3'  G     13 --  O4'  G     13:   95.441  105.500   10.059    0.308 a
<   C3'  U     14 --  O4'  U     14:   95.196  105.500   10.304    0.323 a
<   C3'  G     15 --  O4'  G     15:   92.438  105.500   13.062    0.491 a
<   C3'  G     16 --  O4'  G     16:   98.183  105.500    7.317    0.163 a
<   C3'  A     17 --  O4'  A     17:   95.989  105.500    9.511    0.276 a
<   C3'  A     18 --  O4'  A     18:   98.443  105.500    7.057    0.152 a
<   C3'  C     19 --  O4'  C     19:   95.100  105.500   10.400    0.329 a
<   C3'  A     20 --  O4'  A     20:   91.182  105.500   14.318    0.568 a
<   C3'  G     21 --  O4'  G     21:   95.029  105.500   10.471    0.333 a
<   C3'  C     23 --  O4'  C     23:   98.003  105.500    7.497    0.171 a
<   C3'  G     24 --  O4'  G     24:   96.636  105.500    8.864    0.239 a
<   C3'  U     25 --  O4'  U     25:   98.622  105.500    6.878    0.144 a
<   C3'  G     26 --  O4'  G     26:   91.426  105.500   14.074    0.553 a
<   C3'  U     27 --  O4'  U     27:   93.856  105.500   11.644    0.405 a
<   C3'  U     28 --  O4'  U     28:   94.500  105.500   11.000    0.366 a
<   C3'  C     29 --  O4'  C     29:   93.745  105.500   11.755    0.412 a
<   C3'  G     30 --  O4'  G     30:   95.990  105.500    9.510    0.276 a
<   C3'  G     31 --  O4'  G     31:   92.494  105.500   13.006    0.488 a
<   C3'  A     32 --  O4'  A     32:   92.014  105.500   13.486    0.517 a
<   C3'  A     33 --  O4'  A     33:   97.408  105.500    8.092    0.199 a
<   C3'  C     34 --  O4'  C     34:   94.665  105.500   10.835    0.355 a
<   C3'  A     35 --  O4'  A     35:   96.410  105.500    9.090    0.252 a
<   C3'  C     36 --  O4'  C     36:   92.358  105.500   13.142    0.496 a
<   C3'  C     37 --  O4'  C     37:   94.997  105.500   10.503    0.335 a
<   C3'  C     38 --  O4'  C     38:   97.103  105.500    8.397    0.215 a
<   C3'  G     39 --  O4'  G     39:   97.030  105.500    8.470    0.219 a
<   C3'  G     40 --  O4'  G     40:   96.319  105.500    9.181    0.257 a
<   C3'  C     41 --  O4'  C     41:   97.603  105.500    7.897    0.190 a
<   C3'  C     42 --  O4'  C     42:   94.218  105.500   11.282    0.383 a
<   C3'  G     43 --  O4'  G     43:   93.943  105.500   11.557    0.399 a
<   C3'  C     44 --  O4'  C     44:   93.787  105.500   11.713    0.409 a
<   C3'  A     45 --  O4'  A     45:   94.410  105.500   11.090    0.371 a
<   C3'  A     46 --  O4'  A     46:   95.291  105.500   10.209    0.317 a
<   C3'  C     47 --  O4'  C     47:   93.978  105.500   11.522    0.397 a
<   C3'  C     48 --  O4'  C     48:   95.413  105.500   10.087    0.310 a
<   C3'  C     49 --  O4'  C     49:   94.284  105.500   11.216    0.379 a
<   C3'  U     50 --  O4'  U     50:   91.936  105.500   13.564    0.522 a
<   C3'  G     51 --  O4'  G     51:   93.903  105.500   11.597    0.402 a
<   C3'  G     52 --  O4'  G     52:   94.054  105.500   11.446    0.393 a
<   C3'  G     53 --  O4'  G     53:   96.247  105.500    9.253    0.261 a
<   C3'  A     54 --  O4'  A     54:   90.967  105.500   14.533    0.581 a
<   C3'  G     55 --  O4'  G     55:   94.624  105.500   10.876    0.358 a
<   C3'  A     56 --  O4'  A     56:   91.420  105.500   14.080    0.553 a
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<   C3'  G     58 --  O4'  G     58:   97.550  105.500    7.950    0.193 a
<   C3'  U     59 --  O4'  U     59:   93.978  105.500   11.522    0.397 a
<   C3'  C     60 --  O4'  C     60:   94.255  105.500   11.245    0.380 a
<   C3'  C     61 --  O4'  C     61:   94.181  105.500   11.319    0.385 a
<   C3'  C     62 --  O4'  C     62:   92.914  105.500   12.586    0.462 a
<   C3'  A     63 --  O4'  A     63:   95.211  105.500   10.289    0.322 a
<   C3'  G     64 --  O4'  G     64:   93.807  105.500   11.693    0.408 a
<   C3'  G     65 --  O4'  G     65:   94.555  105.500   10.945    0.362 a
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<   C3'  A     72 --  O4'  A     72:   93.362  105.500   12.138    0.435 a
<   C3'  C     73 --  O4'  C     73:   97.496  105.500    8.004    0.195 a
<   C3'  C     74 --  O4'  C     74:   96.982  105.500    8.518    0.221 a
<   C3'  C     75 --  O4'  C     75:   94.711  105.500   10.789    0.353 a
<   C3'  G     76 --  O4'  G     76:   95.429  105.500   10.071    0.309 a
<   C3'  U     77 --  O4'  U     77:   90.886  105.500   14.614    0.586 a
<   C3'  G     78 --  O4'  G     78:   94.401  105.500   11.099    0.372 a
<   C3'  G     79 --  O4'  G     79:   95.298  105.500   10.202    0.317 a
<   C3'  U     80 --  O4'  U     80:   94.877  105.500   10.623    0.343 a
<   C3'  G     81 --  O4'  G     81:   92.363  105.500   13.137    0.496 a
<   C3'  G     82 --  O4'  G     82:   98.115  105.500    7.385    0.166 a
<   C3'  A     83 --  O4'  A     83:   95.838  105.500    9.662    0.284 a
<   C3'  A     84 --  O4'  A     84:   98.408  105.500    7.092    0.153 a
<   C3'  C     85 --  O4'  C     85:   94.774  105.500   10.726    0.349 a
<   C3'  A     86 --  O4'  A     86:   90.897  105.500   14.603    0.585 a
<   C3'  G     87 --  O4'  G     87:   93.462  105.500   12.038    0.429 a
<   C3'  A     88 --  O4'  A     88:   91.536  105.500   13.964    0.546 a
<   C3'  C     89 --  O4'  C     89:   96.511  105.500    8.989    0.246 a
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<   C3'  U     91 --  O4'  U     91:   93.613  105.500   11.887    0.420 a
<   C3'  G     92 --  O4'  G     92:   91.820  105.500   13.680    0.529 a
<   C3'  U     93 --  O4'  U     93:   93.815  105.500   11.685    0.407 a
<   C3'  U     94 --  O4'  U     94:   94.491  105.500   11.009    0.366 a
<   C3'  C     95 --  O4'  C     95:   93.732  105.500   11.768    0.412 a
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<   C3'  A     98 --  O4'  A     98:   92.110  105.500   13.390    0.511 a
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<   C3'  C    102 --  O4'  C    102:   92.358  105.500   13.142    0.496 a
<   C3'  C    103 --  O4'  C    103:   95.237  105.500   10.263    0.321 a
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<   C3'  C    107 --  O4'  C    107:   97.694  105.500    7.806    0.186 a
<   C3'  C    108 --  O4'  C    108:   94.291  105.500   11.209    0.378 a
<   C3'  G    109 --  O4'  G    109:   93.910  105.500   11.590    0.401 a
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<   C3'  A    111 --  O4'  A    111:   93.827  105.500   11.673    0.407 a
<   C3'  A    112 --  O4'  A    112:   96.222  105.500    9.278    0.262 a
<   C3'  C    113 --  O4'  C    113:   93.783  105.500   11.717    0.409 a
<   C3'  C    114 --  O4'  C    114:   95.359  105.500   10.141    0.313 a
<   C3'  C    115 --  O4'  C    115:   94.278  105.500   11.222    0.379 a
<   C3'  U    116 --  O4'  U    116:   92.009  105.500   13.491    0.517 a
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<   C3'  G    118 --  O4'  G    118:   93.418  105.500   12.082    0.431 a
<   C3'  G    119 --  O4'  G    119:   95.965  105.500    9.535    0.277 a
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<   C4'  U     14 --  C1'  U     14:  117.425  109.300    8.125    0.201 a
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<   C4'  U     25 --  C1'  U     25:  116.714  109.300    7.414    0.167 a
<   C4'  U     27 --  C1'  U     27:  116.651  109.300    7.351    0.165 a
<   C4'  U     28 --  C1'  U     28:  116.555  109.300    7.255    0.160 a
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<   C4'  A     33 --  C1'  A     33:  117.061  109.300    7.761    0.184 a
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<   C4'  G     43 --  C1'  G     43:  116.848  109.300    7.548    0.174 a
<   C4'  C     44 --  C1'  C     44:  116.655  109.300    7.355    0.165 a
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<   C4'  U     50 --  C1'  U     50:  115.582  109.300    6.282    0.120 a
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<   C4'  C    128 --  C1'  C    128:  116.176  109.300    6.876    0.144 a
<   C4'  A    129 --  C1'  A    129:  116.916  109.300    7.616    0.177 a
<   C4'  G    130 --  C1'  G    130:  116.663  109.300    7.363    0.165 a
<   C4'  G    131 --  C1'  G    131:  116.995  109.300    7.695    0.180 a
<   C4'  G3   132 --  C1'  G3   132:  115.734  109.300    6.434    0.126 a
<   C5'  G      2 --  O4'  G      2:  105.579  112.000    6.421    0.126 a
<   C5'  G      5 --  O4'  G      5:  102.258  112.000    9.742    0.289 a
<   C5'  A      6 --  O4'  A      6:  106.058  112.000    5.942    0.108 a
<   C5'  C      9 --  O4'  C      9:  104.724  112.000    7.276    0.161 a
<   C5'  G     13 --  O4'  G     13:  102.433  112.000    9.567    0.279 a
<   C5'  A     20 --  O4'  A     20:  102.437  112.000    9.563    0.279 a
<   C5'  G     31 --  O4'  G     31:  106.079  112.000    5.921    0.107 a
<   C5'  A     33 --  O4'  A     33:  105.867  112.000    6.133    0.115 a
<   C5'  C     42 --  O4'  C     42:  103.283  112.000    8.717    0.231 a
<   C5'  C     49 --  O4'  C     49:  105.390  112.000    6.610    0.133 a
<   C5'  G5    67 --  O4'  G5    67:  105.341  112.000    6.659    0.135 a
<   C5'  G     68 --  O4'  G     68:  105.771  112.000    6.229    0.118 a
<   C5'  C     69 --  O4'  C     69:  106.116  112.000    5.884    0.105 a
<   C5'  G     71 --  O4'  G     71:  102.319  112.000    9.681    0.285 a
<   C5'  A     72 --  O4'  A     72:  104.912  112.000    7.088    0.153 a
<   C5'  C     75 --  O4'  C     75:  105.174  112.000    6.826    0.142 a
<   C5'  G     79 --  O4'  G     79:  102.608  112.000    9.392    0.269 a
<   C5'  G     81 --  O4'  G     81:  104.164  112.000    7.836    0.187 a
<   C5'  A     86 --  O4'  A     86:  102.066  112.000    9.934    0.301 a
<   C5'  G     97 --  O4'  G     97:  105.162  112.000    6.838    0.142 a
<   C5'  A     99 --  O4'  A     99:  105.571  112.000    6.429    0.126 a
<   C5'  C    100 --  O4'  C    100:  106.221  112.000    5.779    0.102 a
<   C5'  C    108 --  O4'  C    108:  103.595  112.000    8.405    0.215 a
<   C5'  C    115 --  O4'  C    115:  105.241  112.000    6.759    0.139 a
<  *HO5' G5     1 --  C5'  G5     1:   85.896  121.000   35.104    1.834 a
<   O3'  G3    66 --  C5'  G5    67:  106.058  121.000   14.942    0.606 a
<                                        Total distance penalty:    379.543
<                                        Total angle    penalty:    139.034
<                                        Total torsion  penalty:      4.028
<  ------------------------------------------------------------------------------
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---------------------------------------
possible FAILURE:  check qmmm.out.dif
/home/progs/amber20/test/middle-scheme/QMMM_Constr_ALA_Methol
33,262c33,34
<  NATOM  =    2428 NTYPES =       9 NBONH =    1616 MBONA  =     410
<  NTHETH =    2832 MTHETA =      11 NPHIH =    1246 MPHIA  =      24
<  NHPARM =       0 NPARM  =       0 NNB   =    6515 NRES   =     404
<  NBONA  =     410 NTHETA =      11 NPHIA =      24 NUMBND =      13
<  NUMANG =      23 NPTRA  =      21 NATYP =      10 NPHB   =       0
<  IFBOX  =       1 NMXRS  =      10 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
< LOADING THE QUANTUM ATOMS AS GROUPS
<      Mask :ACE,ALA,NME; matches    22 atoms
<      BOX TYPE: RECTILINEAR
< --------------------------------------------------------------------------------
<    2.  CONTROL  DATA  FOR  THE  RUN
< --------------------------------------------------------------------------------
< ACE
< General flags:
<      imin    =       0, nmropt  =       0
< Nature and format of input:
<      ntx     =       1, irest   =       0, ntrx    =       1
< Nature and format of output:
<      ntxo    =       2, ntpr    =       1, ntrx    =       1, ntwr    =       1
<      iwrap   =       0, ntwx    =       1, ntwv    =       0, ntwe    =       0
<      ioutfm  =       1, ntwprt  =       0, idecomp =       0, rbornstat=      0
< Potential function:
<      ntf     =       2, 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
< Molecular dynamics:
<      nstlim  =        10, nscm    =      1000, nrespa  =         1
<      t       =   0., dt      =   0.00200, vlimit  =  20.00000
< Initial temperature generation:
<      ig      =    6666
<      tempi   = 300.00000
< 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 =   34.443   Box Y =   37.416   Box Z =   32.412
<      Alpha =   90.000   Beta  =   90.000   Gamma =   90.000
<      NFFT1 =   36       NFFT2 =   40       NFFT3 =   32
<      Cutoff=    8.000   Tol   =0.100E-4
<      Ewald Coefficient =  0.34864
<      Interpolation order =    4
< QMMM options:
<              ifqnt = True       nquant =       22
<               qmgb =        0  qmcharge =        0   adjust_q =        2
<               spin =        1     qmcut =   8.0000    qmshake =        0
<           qmmm_int =        1
<      lnk_atomic_no =        1   lnk_dis =   1.0900 lnk_method =        1
<           qm_theory =     PM3 verbosity =        0
<             qmqmdx = Analytical
<       tight_p_conv = False (converge density to 0.05xSqrt[SCFCRT])
<            scfconv = 0.100E-7  itrmax =     1000
<       printcharges = False      printdipole = False      peptide_corr = False
<     qmmmrij_incore = True
<   qmqm_erep_incore = True
<        pseudo_diag = True pseudo_diag_criteria =   0.0500
<       diag_routine =        0
<           qm_ewald =        1 qm_pme = True
<             kmaxqx =    8 kmaxqy =    8 kmaxqz =    8 ksqmaxq =  100
< --------------------------------------------------------------------------------
<    3.  ATOMIC COORDINATES AND VELOCITIES
< --------------------------------------------------------------------------------
< ACE
<  begin time read from input coords =     0. ps
<  Number of triangulated 3-point waters found:        0
<      Sum of charges from parm topology file =   0.00000022
<      Forcing neutrality...
< QMMM: ADJUSTING CHARGES
< QMMM: ----------------------------------------------------------------------
< QMMM: adjust_q = 2
< QMMM: Uniformly adjusting the charge of MM atoms to conserve total charge.
< QMMM:                             qm_charge =    0
< QMMM: QM atom RESP charge sum (inc MM link) =    0.
< QMMM: Adjusting each MM atom resp charge by =    0.
< QMMM:          Sum of MM + QM region is now =    0.
< QMMM: ----------------------------------------------------------------------
<  ---------------------------------------------------
<  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. to cutoff
<  ---------------------------------------------------
< QMMM: Link Atom Information
< QMMM: ------------------------------------------------------------------------
< QMMM: nlink =     0
< QMMM: ------------------------------------------------------------------------
<   QMMM: QM Region Cartesian Coordinates (*=link atom)
<   QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
<   QMMM:     1        1      H       -2.1116   -3.8239    0.6207
<   QMMM:     2        2      C       -2.1116   -2.7339    0.6207
<   QMMM:     3        3      H       -2.6254   -2.3700    1.5105
<   QMMM:     4        4      H       -2.6254   -2.3700   -0.2691
<   QMMM:     5        5      C       -0.6842   -2.1831    0.6207
<   QMMM:     6        6      O        0.2789   -2.9465    0.6207
<   QMMM:     7        7      N       -0.5563   -0.8542    0.6207
<   QMMM:     8        8      H       -1.3785   -0.2677    0.6207
<   QMMM:     9        9      C        0.7416   -0.2099    0.6207
<   QMMM:    10       10      H        1.2960   -0.5083    1.5105
<   QMMM:    11       11      C        1.5497   -0.6030   -0.6115
<   QMMM:    12       12      H        1.0116   -0.3025   -1.5105
<   QMMM:    13       13      H        2.5189   -0.1049   -0.5851
<   QMMM:    14       14      H        1.6969   -1.6830   -0.6207
<   QMMM:    15       15      C        0.6010    1.3056    0.6207
<   QMMM:    16       16      O       -0.5110    1.8288    0.6207
<   QMMM:    17       17      N        1.7344    2.0110    0.6207
<   QMMM:    18       18      H        2.6254    1.5353    0.6207
<   QMMM:    19       19      C        1.7344    3.4600    0.6207
<   QMMM:    20       20      H        0.7069    3.8239    0.6207
<   QMMM:    21       21      H        2.2482    3.8239    1.5105
<   QMMM:    22       22      H        2.2482    3.8239   -0.2691
< --------------------------------------------------------------------------------
<   3.1 QM CALCULATION INFO
< --------------------------------------------------------------------------------
< QMMM: SINGLET STATE CALCULATION
< QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 29
< --------------------------------------------------------------------------------
<    4.  RESULTS
< --------------------------------------------------------------------------------
<  NSTEP =        0   TIME(PS) =       0.  TEMP(K) =   377.25  PRESS =     0.
<  Etot   =      1809.8386  EKtot   =      2129.0738  EPtot      =      -319.2352
<  BOND   =        44.2720  ANGLE   =       118.2755  DIHED      =       114.6092
<  1-4 NB =         0.  1-4 EEL =      2139.6308  VDWAALS    =      -599.4236
<  EELEC  =     -2050.1411  EHBOND  =         0.  RESTRAINT  =         0.
<  PM3ESCF=       -86.4580
<  Ewald error estimate:   0.2439
<  ------------------------------------------------------------------------------
<  NSTEP =        1   TIME(PS) =       0.002  TEMP(K) =   290.49  PRESS =     0.
<  Etot   =      1320.2082  EKtot   =      1639.4435  EPtot      =      -319.2352
<  BOND   =        44.2720  ANGLE   =       118.2755  DIHED      =       114.6092
<  1-4 NB =         0.  1-4 EEL =      2139.6308  VDWAALS    =      -599.4236
<  EELEC  =     -2050.1411  EHBOND  =         0.  RESTRAINT  =         0.
<  PM3ESCF=       -86.4580
<  Ewald error estimate:   0.2439
<  ------------------------------------------------------------------------------
<  NSTEP =        2   TIME(PS) =       0.004  TEMP(K) =   262.04  PRESS =     0.
<  Etot   =      1330.2103  EKtot   =      1478.8308  EPtot      =      -148.6205
<  BOND   =        58.4859  ANGLE   =       266.8667  DIHED      =       113.8676
<  1-4 NB =         0.  1-4 EEL =      2136.0454  VDWAALS    =      -599.1342
<  EELEC  =     -2040.3697  EHBOND  =         0.  RESTRAINT  =         0.
<  PM3ESCF=       -84.3821
<  Ewald error estimate:   0.2451
<  ------------------------------------------------------------------------------
<  NSTEP =        3   TIME(PS) =       0.006  TEMP(K) =   207.14  PRESS =     0.
<  Etot   =      1355.3046  EKtot   =      1169.0127  EPtot      =       186.2919
<  BOND   =        90.1318  ANGLE   =       560.5526  DIHED      =       114.1333
<  1-4 NB =         0.  1-4 EEL =      2133.2552  VDWAALS    =      -597.1079
<  EELEC  =     -2027.3737  EHBOND  =         0.  RESTRAINT  =         0.
<  PM3ESCF=       -87.2995
<  Ewald error estimate:   0.2471
<  ------------------------------------------------------------------------------
<  NSTEP =        4   TIME(PS) =       0.008  TEMP(K) =   177.14  PRESS =     0.
<  Etot   =      1374.5566  EKtot   =       999.7026  EPtot      =       374.8540
<  BOND   =       115.3584  ANGLE   =       715.2287  DIHED      =       115.1810
<  1-4 NB =         0.  1-4 EEL =      2130.3024  VDWAALS    =      -595.1609
<  EELEC  =     -2021.0112  EHBOND  =         0.  RESTRAINT  =         0.
<  PM3ESCF=       -85.0446
<  Ewald error estimate:   0.2480
<  ------------------------------------------------------------------------------
<  NSTEP =        5   TIME(PS) =       0.010  TEMP(K) =   195.85  PRESS =     0.
<  Etot   =      1377.4211  EKtot   =      1105.2835  EPtot      =       272.1376
<  BOND   =       120.6483  ANGLE   =       606.0059  DIHED      =       116.7074
<  1-4 NB =         0.  1-4 EEL =      2127.0460  VDWAALS    =      -594.2198
<  EELEC  =     -2023.7597  EHBOND  =         0.  RESTRAINT  =         0.
<  PM3ESCF=       -80.2905
<  Ewald error estimate:   0.2471
<  ------------------------------------------------------------------------------
<  NSTEP =        6   TIME(PS) =       0.012  TEMP(K) =   238.83  PRESS =     0.
<  Etot   =      1364.6043  EKtot   =      1347.8671  EPtot      =        16.7372
<  BOND   =       110.2746  ANGLE   =       374.2873  DIHED      =       118.3661
<  1-4 NB =         0.  1-4 EEL =      2124.5230  VDWAALS    =      -593.1813
<  EELEC  =     -2032.6514  EHBOND  =         0.  RESTRAINT  =         0.
<  PM3ESCF=       -84.8811
<  Ewald error estimate:   0.2456
<  ------------------------------------------------------------------------------
<  NSTEP =        7   TIME(PS) =       0.014  TEMP(K) =   261.31  PRESS =     0.
<  Etot   =      1360.4484  EKtot   =      1474.7459  EPtot      =      -114.2974
<  BOND   =        97.4874  ANGLE   =       260.2066  DIHED      =       120.0378
<  1-4 NB =         0.  1-4 EEL =      2123.9003  VDWAALS    =      -590.9559
<  EELEC  =     -2041.8000  EHBOND  =         0.  RESTRAINT  =         0.
<  PM3ESCF=       -83.1737
<  Ewald error estimate:   0.2447
<  ------------------------------------------------------------------------------
<  NSTEP =        8   TIME(PS) =       0.016  TEMP(K) =   249.52  PRESS =     0.
<  Etot   =      1376.3539  EKtot   =      1408.2167  EPtot      =       -31.8628
<  BOND   =        90.3359  ANGLE   =       354.7743  DIHED      =       121.7162
<  1-4 NB =         0.  1-4 EEL =      2125.4566  VDWAALS    =      -588.3791
<  EELEC  =     -2047.5720  EHBOND  =         0.  RESTRAINT  =         0.
<  PM3ESCF=       -88.1946
<  Ewald error estimate:   0.2450
<  ------------------------------------------------------------------------------
<  NSTEP =        9   TIME(PS) =       0.018  TEMP(K) =   225.07  PRESS =     0.
<  Etot   =      1405.3944  EKtot   =      1270.2035  EPtot      =       135.1909
<  BOND   =        85.4588  ANGLE   =       527.8056  DIHED      =       123.3109
<  1-4 NB =         0.  1-4 EEL =      2128.3614  VDWAALS    =      -587.4098
<  EELEC  =     -2051.6725  EHBOND  =         0.  RESTRAINT  =         0.
<  PM3ESCF=       -90.6634
<  Ewald error estimate:   0.2457
<  ------------------------------------------------------------------------------
<  NSTEP =       10   TIME(PS) =       0.020  TEMP(K) =   216.99  PRESS =     0.
<  Etot   =      1415.9829  EKtot   =      1224.6233  EPtot      =       191.3596
<  BOND   =        78.6648  ANGLE   =       589.7328  DIHED      =       124.5595
<  1-4 NB =         0.  1-4 EEL =      2131.3726  VDWAALS    =      -588.9306
<  EELEC  =     -2057.0615  EHBOND  =         0.  RESTRAINT  =         0.
<  PM3ESCF=       -86.9781
<  Ewald error estimate:   0.2456
<  ------------------------------------------------------------------------------
<       A V E R A G E S   O V E R      10 S T E P S
<  NSTEP =       10   TIME(PS) =       0.020  TEMP(K) =   232.44  PRESS =     0.
<  Etot   =      1368.0485  EKtot   =      1311.7930  EPtot      =        56.2555
<  BOND   =        89.1118  ANGLE   =       437.3736  DIHED      =       118.2489
<  1-4 NB =         0.  1-4 EEL =      2129.9894  VDWAALS    =      -593.3903
<  EELEC  =     -2039.3413  EHBOND  =         0.  RESTRAINT  =         0.
<  PM3ESCF=       -85.7366
<  Ewald error estimate:   0.2458
<  ------------------------------------------------------------------------------
<       R M S  F L U C T U A T I O N S
<  NSTEP =       10   TIME(PS) =       0.020  TEMP(K) =    32.78  PRESS =     0.
<  Etot   =        28.0072  EKtot   =       184.9784  EPtot      =       202.7032
<  BOND   =        22.9674  ANGLE   =       180.3584  DIHED      =         3.7663
<  1-4 NB =         0.  1-4 EEL =         4.9105  VDWAALS    =         4.1686
<  EELEC  =        11.9344  EHBOND  =         0.  RESTRAINT  =         0.
<  PM3ESCF=         2.7220
<  Ewald error estimate:   0.1178E-2
<  ------------------------------------------------------------------------------
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---
> ERROR: I could not find the number of atoms or the time on
>        the second line of your inpcrd file [ala.crd]. Bad INPCRD file!
---------------------------------------
possible FAILURE:  check invalid_atom_ids.out.dif
/home/progs/amber20/test/qmmm2/input_validation
18,28d17
<  NATOM  =      22 NTYPES =       8 NBONH =      13 MBONA  =       8
<  NTHETH =      30 MTHETA =       8 NPHIH =      44 MPHIA  =       7
<  NHPARM =       0 NPARM  =       0 NNB   =     112 NRES   =       1
<  NBONA  =       8 NTHETA =       8 NPHIA =       7 NUMBND =      10
<  NUMANG =      17 NPTRA  =       2 NATYP =       9 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      22 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  QM ATOM VALIDATION: iqmatom ID number of       27 is not valid.
<  SANDER BOMB in subroutine validate_qm_atoms
<  invalid QM atom ID
<  Need 0 < QM atom ID <= natom
---------------------------------------
possible FAILURE:  check non-unique.out.dif
/home/progs/amber20/test/qmmm2/input_validation
18,28d17
<  NATOM  =      22 NTYPES =       8 NBONH =      13 MBONA  =       8
<  NTHETH =      30 MTHETA =       8 NPHIH =      44 MPHIA  =       7
<  NHPARM =       0 NPARM  =       0 NNB   =     112 NRES   =       1
<  NBONA  =       8 NTHETA =       8 NPHIA =       7 NUMBND =      10
<  NUMANG =      17 NPTRA  =       2 NATYP =       9 NPHB   =       0
<  IFBOX  =       0 NMXRS  =      22 IFCAP =       0 NEXTRA =       0
<  NCOPY  =       0
<  QM ATOM VALIDATION: qm atom        7 is not unique.
<  SANDER BOMB in subroutine validate_qm_atoms
<  QM atoms specified with iqmatoms do not form a unique set.
<  Require a unique list of qm atom numbers
---------------------------------------
possible FAILURE:  check min.out.dif
/home/progs/amber20/test/sebomd/AM1-d-PhoT/nucleoside
---------------------------------------
possible FAILURE:  check md.out.dif
/home/progs/amber20/test/sebomd/AM1-d-PhoT/nucleoside
---------------------------------------
