Sun Oct 9 02:01:55 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 Sun Oct 9 2011 at 02:01:55 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 = 1868 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6587713 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): 87.35300 139.2990 ymin,ymax (A): 113.5130 150.9480 zmin,zma (A): 35.22800 89.26800 x,y,z range (A): 51.94601 37.43500 54.04000 scale (grids/A): 0.6587713 object centre (A): 113.3260 132.2305 62.24800 number of atom coordinates read : 1868 total number of charged atoms : 1732 net assigned charge : 6.500015 assigned positive charge : 271.2522 centred at (gu) : 88.42737 90.23401 89.42059 assigned negative charge : -264.7524 centred at (gu) : 88.53728 90.22002 89.49869 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5559 nv = 96 ne = 84 npr = 36770 no. pairs analyzed = 36770 no. exposed pairs = 2782 no. arc points = 20006 no. surface atoms = 928 nbur = 940 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 344 mr = 2569 m= 0 mr = 37 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1839 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6333 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8998334E-08 4.8297495E-09 midg,1,midg; midg,igrid,midg 1.3172453E-08 1.8295072E-08 1,midg,midg; igrid,midg,midg 4.1361165E-08 1.0150181E-09 gauss-seidel spectral radius is 0.9880021 estimated iterations to convergence 75 setup time was (sec) 0.5000000 now iterating at: 02:01:56 rms-change max change #iterations 0.1363922 22.47324 at 10iterations 1.4527733E-02 2.188225 at 20iterations 1.6103731E-03 0.2704649 at 30iterations 2.5542852E-04 3.6278725E-02 at 40iterations 6.1344872E-05 8.2855225E-03 at 50iterations finished qdiffx linear iterations at : 02:01:59 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 6.1344872E-05 8.2855225E-03 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 02:02:00 4.434u 0.417s 0:05.14 94.1% 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 Sun Oct 9 2011 at 02:02:00 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 = 1868 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.976314 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): 87.35300 139.2990 ymin,ymax (A): 113.5130 150.9480 zmin,zma (A): 35.22800 89.26800 x,y,z range (A): 51.94601 37.43500 54.04000 scale (grids/A): 1.976314 object centre (A): 113.3260 132.2305 62.24800 number of atom coordinates read : 1868 total number of charged atoms : 1732 net assigned charge : 6.500015 assigned positive charge : 271.2522 centred at (gu) : 85.28238 90.70202 88.26203 assigned negative charge : -264.7524 centred at (gu) : 85.61208 90.66042 88.49638 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 58620 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20006 grid for indexing accessible points = 1.400000 m= 20540 mr = 36851 m= 3459 mr = 13707 m= 220 mr = 1849 m= 5 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 30384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 13666 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) : 0.6587713 object centre at (A) : 113.3260 132.2305 62.24800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9615627E-02 2.0392889E-02 midg,1,midg; midg,igrid,midg 1.4271331E-02 1.2135641E-02 1,midg,midg; igrid,midg,midg 2.0197917E-02 -2.7427606E-02 gauss-seidel spectral radius is 0.9986734 estimated iterations to convergence 218 setup time was (sec) 0.7900000 now iterating at: 02:02:01 rms-change max change #iterations 3.716491 202.9010 at 10iterations 1.746699 70.54541 at 20iterations 0.8224800 36.21511 at 30iterations 0.3883237 13.93994 at 40iterations 0.1838723 6.704948 at 50iterations 8.6553536E-02 2.987493 at 60iterations 4.0906399E-02 1.436054 at 70iterations 1.9458666E-02 0.6749392 at 80iterations 9.2093656E-03 0.3130046 at 90iterations 4.4090208E-03 0.1588898 at 100iterations 2.1323382E-03 8.2255840E-02 at 110iterations 1.0563195E-03 3.9539337E-02 at 120iterations finished qdiffx linear iterations at : 02:02:11 total time elapsed so far: 10.15000 # loops : 120 mean,max change (kT/e) : 1.0563195E-03 3.9539337E-02 energy calculations done at 10.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.32000 DelPhi exited at 02:02:11 10.327u 0.465s 0:11.07 97.3% 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 Sun Oct 9 2011 at 02:02:11 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 = 1868 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.964471 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): 87.35300 139.2990 ymin,ymax (A): 113.5130 150.9480 zmin,zma (A): 35.22800 89.26800 x,y,z range (A): 51.94601 37.43500 54.04000 scale (grids/A): 2.964471 object centre (A): 113.3260 132.2305 62.24800 number of atom coordinates read : 1868 total number of charged atoms : 1732 net assigned charge : 6.500015 assigned positive charge : 271.2522 centred at (gu) : 82.92357 91.05319 87.39306 assigned negative charge : -264.7524 centred at (gu) : 83.41816 90.99077 87.74469 start vw surface at 0.1100000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 135330 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20006 grid for indexing accessible points = 1.400000 m= 64392 mr = 90215 m= 24081 mr = 49563 m= 6294 mr = 17999 m= 954 mr = 4258 m= 56 mr = 509 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.300000 number of dielectric boundary points 68545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 13855 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) : 1.976314 object centre at (A) : 113.3260 132.2305 62.24800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3851562 0.3683504 midg,1,midg; midg,igrid,midg 0.1221832 9.5202856E-02 1,midg,midg; igrid,midg,midg 0.1383604 -0.3854207 gauss-seidel spectral radius is 0.9992765 estimated iterations to convergence 293 setup time was (sec) 1.630000 now iterating at: 02:02:13 rms-change max change #iterations 8.866119 409.9792 at 10iterations 5.274810 161.7634 at 20iterations 3.127449 97.55568 at 30iterations 1.844688 41.42232 at 40iterations 1.083052 24.40113 at 50iterations 0.6331743 13.47190 at 60iterations 0.3692719 7.778468 at 70iterations 0.2152662 4.819345 at 80iterations 0.1252114 3.217120 at 90iterations 7.2827153E-02 1.589355 at 100iterations 4.2392053E-02 0.9426193 at 110iterations 2.4563877E-02 0.4870396 at 120iterations 1.4219510E-02 0.3027954 at 130iterations 8.3016828E-03 0.1833844 at 140iterations 4.8175901E-03 9.7312927E-02 at 150iterations 2.8113734E-03 5.4450989E-02 at 160iterations 1.6576230E-03 3.6533356E-02 at 170iterations 9.8595116E-04 2.1736145E-02 at 180iterations finished qdiffx linear iterations at : 02:02:29 total time elapsed so far: 17.18000 # loops : 180 mean,max change (kT/e) : 9.8595116E-04 2.1736145E-02 energy calculations done at 17.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.35000 DelPhi exited at 02:02:29 17.350u 0.470s 0:18.08 98.5% 0+0k 0+0io 0pf+0w