Mon Oct 10 17:05:55 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+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 Mon Oct 10 2011 at 17:05:55 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1951 !!! WARNING: HIT 148 has a net charge of 0.5140 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: 0.6528756 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): 25.85200 76.90100 ymin,ymax (A): 7.921999 56.10100 zmin,zma (A): -11.64800 42.88000 x,y,z range (A): 51.04900 48.17900 54.52800 scale (grids/A): 0.6528756 object centre (A): 51.37650 32.01150 15.61600 number of atom coordinates read : 1951 total number of charged atoms : 1819 net assigned charge : -7.485983 assigned positive charge : 285.1500 centred at (gu) : 89.52327 88.47585 87.88570 assigned negative charge : -292.6359 centred at (gu) : 89.79288 88.67271 88.29570 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5685 nv = 96 ne = 84 npr = 39784 no. pairs analyzed = 39784 no. exposed pairs = 2652 no. arc points = 19303 no. surface atoms = 897 nbur = 1054 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 266 mr = 2771 m= 0 mr = 21 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2600000 number of dielectric boundary points 3159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1840 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6593 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0102333E-08 -4.4983238E-08 midg,1,midg; midg,igrid,midg 9.6298649E-09 -3.0553849E-08 1,midg,midg; igrid,midg,midg 1.6923059E-08 -4.6500212E-08 gauss-seidel spectral radius is 0.9877943 estimated iterations to convergence 74 setup time was (sec) 0.5800000 now iterating at: 17:05:56 rms-change max change #iterations 0.1475629 25.33068 at 10iterations 1.4964960E-02 2.368286 at 20iterations 1.5429102E-03 0.2637405 at 30iterations 1.5976735E-04 2.8640747E-02 at 40iterations 1.6061513E-05 2.4185181E-03 at 50iterations finished qdiffx linear iterations at : 17:06:00 total time elapsed so far: 4.360000 # loops : 50 mean,max change (kT/e) : 1.6061513E-05 2.4185181E-03 energy calculations done at 4.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 17:06:00 4.532u 0.414s 0:05.33 92.6% 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 17:06:00 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1951 !!! WARNING: HIT 148 has a net charge of 0.5140 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: 1.958627 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): 25.85200 76.90100 ymin,ymax (A): 7.921999 56.10100 zmin,zma (A): -11.64800 42.88000 x,y,z range (A): 51.04900 48.17900 54.52800 scale (grids/A): 1.958627 object centre (A): 51.37650 32.01150 15.61600 number of atom coordinates read : 1951 total number of charged atoms : 1819 net assigned charge : -7.485983 assigned positive charge : 285.1500 centred at (gu) : 88.56994 85.42749 83.65716 assigned negative charge : -292.6359 centred at (gu) : 89.37852 86.01797 84.88700 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 61084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19303 grid for indexing accessible points = 1.400000 m= 19568 mr = 39312 m= 2690 mr = 13463 m= 154 mr = 1492 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 787 time to turn everything in is 0.5200000 number of dielectric boundary points 29187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 14359 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) : 0.6528756 object centre at (A) : 51.37650 32.01150 15.61600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0906627E-02 -4.9045768E-02 midg,1,midg; midg,igrid,midg 2.5883880E-02 -1.3264342E-02 1,midg,midg; igrid,midg,midg -3.5705991E-02 -4.5446418E-02 gauss-seidel spectral radius is 0.9986486 estimated iterations to convergence 216 setup time was (sec) 0.8200000 now iterating at: 17:06:02 rms-change max change #iterations 3.866456 215.2728 at 10iterations 1.811445 66.08436 at 20iterations 0.8473940 30.88827 at 30iterations 0.3972383 14.01645 at 40iterations 0.1853138 6.320409 at 50iterations 8.7443009E-02 3.293301 at 60iterations 4.0789094E-02 1.528442 at 70iterations 1.9118140E-02 0.6811832 at 80iterations 8.9712385E-03 0.3228455 at 90iterations 4.2081932E-03 0.1459990 at 100iterations 1.9705063E-03 6.5238953E-02 at 110iterations 9.2181255E-04 3.1616211E-02 at 120iterations finished qdiffx linear iterations at : 17:06:11 total time elapsed so far: 10.57000 # loops : 120 mean,max change (kT/e) : 9.2181255E-04 3.1616211E-02 energy calculations done at 10.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.80000 DelPhi exited at 17:06:12 10.805u 0.448s 0:11.64 96.5% 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 17:06:12 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1951 !!! WARNING: HIT 148 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.937940 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): 25.85200 76.90100 ymin,ymax (A): 7.921999 56.10100 zmin,zma (A): -11.64800 42.88000 x,y,z range (A): 51.04900 48.17900 54.52800 scale (grids/A): 2.937940 object centre (A): 51.37650 32.01150 15.61600 number of atom coordinates read : 1951 total number of charged atoms : 1819 net assigned charge : -7.485983 assigned positive charge : 285.1500 centred at (gu) : 87.85484 83.14122 80.48572 assigned negative charge : -292.6359 centred at (gu) : 89.06772 84.02693 82.33050 start vw surface at 0.1000000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 141225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19303 grid for indexing accessible points = 1.400000 m= 64962 mr = 96265 m= 21449 mr = 50901 m= 4472 mr = 16360 m= 560 mr = 2996 m= 25 mr = 341 m= 0 mr = 10 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 2595 time to turn everything in is 1.290000 number of dielectric boundary points 65820 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 14552 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) : 1.958627 object centre at (A) : 51.37650 32.01150 15.61600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5283912 -0.4056906 midg,1,midg; midg,igrid,midg 0.2507708 -0.1389432 1,midg,midg; igrid,midg,midg -0.5422658 -0.4649726 gauss-seidel spectral radius is 0.9992660 estimated iterations to convergence 291 setup time was (sec) 1.630000 now iterating at: 17:06:14 rms-change max change #iterations 9.090692 484.2474 at 10iterations 5.289152 159.7213 at 20iterations 3.070699 69.35894 at 30iterations 1.772832 39.79685 at 40iterations 1.019850 21.11336 at 50iterations 0.5877885 12.12619 at 60iterations 0.3380572 6.970318 at 70iterations 0.1943229 3.835932 at 80iterations 0.1114137 2.202976 at 90iterations 6.3979931E-02 1.318260 at 100iterations 3.6842968E-02 0.7651730 at 110iterations 2.1200417E-02 0.4185205 at 120iterations 1.2138174E-02 0.2384720 at 130iterations 6.9798641E-03 0.1355286 at 140iterations 4.0098685E-03 7.9528809E-02 at 150iterations 2.3022548E-03 4.5700073E-02 at 160iterations 1.3207248E-03 2.6100159E-02 at 170iterations 7.6067500E-04 1.5840471E-02 at 180iterations finished qdiffx linear iterations at : 17:06:31 total time elapsed so far: 17.94000 # loops : 180 mean,max change (kT/e) : 7.6067500E-04 1.5840471E-02 energy calculations done at 17.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.11000 DelPhi exited at 17:06:31 18.112u 0.480s 0:19.19 96.8% 0+0k 0+0io 0pf+0w