Mon Oct 10 19:33:38 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+sph.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 = amb.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 Mon Oct 10 2011 at 19:33:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2291 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7029461 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): -41.10200 4.341000 ymin,ymax (A): -23.75000 26.89400 zmin,zma (A): 32.49800 82.41300 x,y,z range (A): 45.44300 50.64400 49.91500 scale (grids/A): 0.7029461 object centre (A): -18.38050 1.572000 57.45550 number of atom coordinates read : 2291 total number of charged atoms : 2155 net assigned charge : 2.000003 assigned positive charge : 339.2971 centred at (gu) : 89.16138 87.46019 88.33253 assigned negative charge : -337.2977 centred at (gu) : 89.12240 87.60114 88.25663 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7618 nv = 96 ne = 84 npr = 47141 no. pairs analyzed = 47141 no. exposed pairs = 2820 no. arc points = 20204 no. surface atoms = 947 nbur = 1344 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 524 mr = 4243 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2800000 number of dielectric boundary points 3838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1825 ## 138 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8622 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2100594E-08 3.6146496E-08 midg,1,midg; midg,igrid,midg 1.3433905E-07 -3.2624047E-08 1,midg,midg; igrid,midg,midg -5.7604019E-09 2.7688174E-08 gauss-seidel spectral radius is 0.9894785 estimated iterations to convergence 79 setup time was (sec) 0.5300000 now iterating at: 19:33:40 rms-change max change #iterations 0.2055508 30.98803 at 10iterations 2.5137974E-02 3.071175 at 20iterations 3.0102609E-03 0.3621197 at 30iterations 3.6922991E-04 4.3848038E-02 at 40iterations 4.5665147E-05 6.5374374E-03 at 50iterations finished qdiffx linear iterations at : 19:33:42 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 4.5665147E-05 6.5374374E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 19:33:43 3.523u 0.200s 0:04.04 92.0% 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 Mon Oct 10 2011 at 19:33:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2291 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.108838 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): -41.10200 4.341000 ymin,ymax (A): -23.75000 26.89400 zmin,zma (A): 32.49800 82.41300 x,y,z range (A): 45.44300 50.64400 49.91500 scale (grids/A): 2.108838 object centre (A): -18.38050 1.572000 57.45550 number of atom coordinates read : 2291 total number of charged atoms : 2155 net assigned charge : 2.000003 assigned positive charge : 339.2971 centred at (gu) : 87.48354 82.38028 84.99707 assigned negative charge : -337.2977 centred at (gu) : 87.36690 82.80317 84.76963 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 80235 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20204 grid for indexing accessible points = 1.400000 m= 31670 mr = 55366 m= 6422 mr = 23687 m= 537 mr = 4184 m= 12 mr = 218 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1625 time to turn everything in is 0.6600000 number of dielectric boundary points 35421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17131 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) : 0.7029461 object centre at (A) : -18.38050 1.572000 57.45550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2114257E-03 4.4265192E-02 midg,1,midg; midg,igrid,midg 5.1322646E-02 -1.8486658E-02 1,midg,midg; igrid,midg,midg 1.4742853E-02 1.4218703E-02 gauss-seidel spectral radius is 0.9988410 estimated iterations to convergence 232 setup time was (sec) 0.9600000 now iterating at: 19:33:44 rms-change max change #iterations 4.794563 209.4561 at 10iterations 2.376462 85.99684 at 20iterations 1.180794 41.58881 at 30iterations 0.5856900 16.58975 at 40iterations 0.2914124 8.151737 at 50iterations 0.1448261 4.213026 at 60iterations 7.2149403E-02 2.028435 at 70iterations 3.5703611E-02 1.078127 at 80iterations 1.7863935E-02 0.4981461 at 90iterations 8.8398103E-03 0.2528305 at 100iterations 4.3829363E-03 0.1521530 at 110iterations 2.1809961E-03 6.6537857E-02 at 120iterations finished qdiffx linear iterations at : 19:33:51 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 2.1809961E-03 6.6537857E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.110000 DelPhi exited at 19:33:52 8.109u 0.224s 0:08.80 94.5% 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 Mon Oct 10 2011 at 19:33:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2291 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.163257 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): -41.10200 4.341000 ymin,ymax (A): -23.75000 26.89400 zmin,zma (A): 32.49800 82.41300 x,y,z range (A): 45.44300 50.64400 49.91500 scale (grids/A): 3.163257 object centre (A): -18.38050 1.572000 57.45550 number of atom coordinates read : 2291 total number of charged atoms : 2155 net assigned charge : 2.000003 assigned positive charge : 339.2971 centred at (gu) : 86.22520 78.57032 82.49561 assigned negative charge : -337.2977 centred at (gu) : 86.05032 79.20469 82.15453 start vw surface at 0.1400000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 185367 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20204 grid for indexing accessible points = 1.400000 m= 97079 mr = 133885 m= 40998 mr = 79799 m= 12063 mr = 33536 m= 2136 mr = 9212 m= 158 mr = 1409 m= 2 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 5469 time to turn everything in is 2.010000 number of dielectric boundary points 79899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 17236 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) : 2.108838 object centre at (A) : -18.38050 1.572000 57.45550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8718558E-03 0.8125806 midg,1,midg; midg,igrid,midg 0.4283472 -7.2594866E-02 1,midg,midg; igrid,midg,midg 0.2155269 3.3464327E-02 gauss-seidel spectral radius is 0.9993086 estimated iterations to convergence 300 setup time was (sec) 2.340000 now iterating at: 19:33:54 rms-change max change #iterations 10.85518 360.3895 at 10iterations 6.466386 175.8116 at 20iterations 3.829511 73.99590 at 30iterations 2.265580 73.10211 at 40iterations 1.338899 28.15059 at 50iterations 0.7884453 14.08936 at 60iterations 0.4641222 8.254044 at 70iterations 0.2725701 5.172172 at 80iterations 0.1598801 2.829786 at 90iterations 9.4036162E-02 1.683268 at 100iterations 5.5084690E-02 0.9388933 at 110iterations 3.2356717E-02 0.5398502 at 120iterations 1.8950319E-02 0.3191519 at 130iterations 1.1101652E-02 0.1881933 at 140iterations 6.4908699E-03 0.1045055 at 150iterations 3.7994334E-03 6.0009629E-02 at 160iterations 2.2303928E-03 3.5255432E-02 at 170iterations 1.3054884E-03 2.2149086E-02 at 180iterations finished qdiffx linear iterations at : 19:34:06 total time elapsed so far: 13.60000 # loops : 180 mean,max change (kT/e) : 1.3054884E-03 2.2149086E-02 energy calculations done at 13.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 19:34:06 13.800u 0.239s 0:14.52 96.6% 0+0k 0+0io 0pf+0w