Tue Oct 11 05:28:18 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 05:28:18 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2093 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7130410 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 25.71400 72.30900 ymin,ymax (A): -19.90200 30.02500 zmin,zma (A): 3.789000 46.13300 x,y,z range (A): 46.59500 49.92700 42.34400 scale (grids/A): 0.7130410 object centre (A): 49.01150 5.061500 24.96100 number of atom coordinates read : 2093 total number of charged atoms : 1970 net assigned charge : 5.564011 assigned positive charge : 322.8461 centred at (gu) : 89.18600 90.94314 90.25249 assigned negative charge : -317.2821 centred at (gu) : 89.28584 90.86501 90.35086 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7153 nv = 96 ne = 84 npr = 42340 no. pairs analyzed = 42340 no. exposed pairs = 2558 no. arc points = 17113 no. surface atoms = 882 nbur = 1211 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 461 mr = 4127 m= 3 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1591 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8012 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0299154E-07 -4.1387365E-09 midg,1,midg; midg,igrid,midg 7.0925532E-09 1.1611662E-07 1,midg,midg; igrid,midg,midg 1.2751786E-07 -3.5000169E-09 gauss-seidel spectral radius is 0.9897443 estimated iterations to convergence 80 setup time was (sec) 0.3500000 now iterating at: 05:28:18 rms-change max change #iterations 0.2158295 29.39772 at 10iterations 2.7530024E-02 3.936040 at 20iterations 3.8073310E-03 0.5700684 at 30iterations 7.0435274E-04 8.9286804E-02 at 40iterations 2.0388389E-04 2.4549484E-02 at 50iterations finished qdiffx linear iterations at : 05:28:21 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 2.0388389E-04 2.4549484E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 05:28:22 3.339u 0.169s 0:03.87 90.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 05:28:22 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2093 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.139123 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 25.71400 72.30900 ymin,ymax (A): -19.90200 30.02500 zmin,zma (A): 3.789000 46.13300 x,y,z range (A): 46.59500 49.92700 42.34400 scale (grids/A): 2.139123 object centre (A): 49.01150 5.061500 24.96100 number of atom coordinates read : 2093 total number of charged atoms : 1970 net assigned charge : 5.564011 assigned positive charge : 322.8461 centred at (gu) : 87.55775 92.82975 90.75774 assigned negative charge : -317.2821 centred at (gu) : 87.85752 92.59508 91.05276 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75709 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17113 grid for indexing accessible points = 1.400000 m= 30919 mr = 54022 m= 5883 mr = 23626 m= 579 mr = 3973 m= 17 mr = 293 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 31193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15646 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.7130410 object centre at (A) : 49.01150 5.061500 24.96100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9625786E-02 2.0485785E-02 midg,1,midg; midg,igrid,midg 2.4494108E-02 3.9272573E-02 1,midg,midg; igrid,midg,midg 4.1492201E-02 -3.7572816E-02 gauss-seidel spectral radius is 0.9988441 estimated iterations to convergence 233 setup time was (sec) 0.6100000 now iterating at: 05:28:23 rms-change max change #iterations 4.778224 211.7942 at 10iterations 2.369716 74.71539 at 20iterations 1.185200 36.22127 at 30iterations 0.5912116 18.24880 at 40iterations 0.2942691 8.905446 at 50iterations 0.1470639 4.430946 at 60iterations 7.3188081E-02 1.989735 at 70iterations 3.6656193E-02 1.107716 at 80iterations 1.8519226E-02 0.5488420 at 90iterations 9.3642604E-03 0.3167667 at 100iterations 4.8090480E-03 0.1460199 at 110iterations 2.5502110E-03 7.0950508E-02 at 120iterations finished qdiffx linear iterations at : 05:28:30 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.5502110E-03 7.0950508E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 05:28:31 7.775u 0.187s 0:08.76 90.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 05:28:31 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2093 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.208684 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 25.71400 72.30900 ymin,ymax (A): -19.90200 30.02500 zmin,zma (A): 3.789000 46.13300 x,y,z range (A): 46.59500 49.92700 42.34400 scale (grids/A): 3.208684 object centre (A): 49.01150 5.061500 24.96100 number of atom coordinates read : 2093 total number of charged atoms : 1970 net assigned charge : 5.564011 assigned positive charge : 322.8461 centred at (gu) : 86.33663 94.24452 91.13669 assigned negative charge : -317.2821 centred at (gu) : 86.78638 93.89259 91.57913 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 174516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17113 grid for indexing accessible points = 1.400000 m= 96174 mr = 129932 m= 39193 mr = 80410 m= 11109 mr = 32343 m= 2253 mr = 8645 m= 274 mr = 1648 m= 12 mr = 181 m= 0 mr = 3 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 70369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 15760 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.139123 object centre at (A) : 49.01150 5.061500 24.96100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1955589 0.1725794 midg,1,midg; midg,igrid,midg 0.1653709 0.2859247 1,midg,midg; igrid,midg,midg 0.3981503 -0.4087743 gauss-seidel spectral radius is 0.9992999 estimated iterations to convergence 298 setup time was (sec) 1.420000 now iterating at: 05:28:32 rms-change max change #iterations 10.58967 342.7098 at 10iterations 6.278680 183.5728 at 20iterations 3.731726 85.07454 at 30iterations 2.209119 42.65838 at 40iterations 1.304977 24.46269 at 50iterations 0.7681012 15.08639 at 60iterations 0.4528894 9.925854 at 70iterations 0.2662415 5.017793 at 80iterations 0.1565471 2.776678 at 90iterations 9.2240945E-02 1.586686 at 100iterations 5.4355249E-02 0.9309158 at 110iterations 3.2132708E-02 0.5968475 at 120iterations 1.9119371E-02 0.3449364 at 130iterations 1.1599940E-02 0.2111206 at 140iterations 7.2437059E-03 0.1398163 at 150iterations 4.7100121E-03 8.4208012E-02 at 160iterations 3.2462408E-03 6.0287476E-02 at 170iterations 2.3797783E-03 4.2968750E-02 at 180iterations finished qdiffx linear iterations at : 05:28:43 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 2.3797783E-03 4.2968750E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 05:28:44 12.775u 0.202s 0:13.56 95.6% 0+0k 0+0io 0pf+0w