Sun Oct 9 12:21:36 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 Sun Oct 9 2011 at 12:21:36 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2411 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: 0.6864901 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): -14.32300 37.35800 ymin,ymax (A): -1.185000 44.82800 zmin,zma (A): -8.213000 43.64500 x,y,z range (A): 51.68100 46.01300 51.85800 scale (grids/A): 0.6864901 object centre (A): 11.51750 21.82150 17.71600 number of atom coordinates read : 2411 total number of charged atoms : 2269 net assigned charge : 3.500025 assigned positive charge : 373.1932 centred at (gu) : 90.87620 91.47647 90.39854 assigned negative charge : -369.6935 centred at (gu) : 91.07114 91.54314 90.37444 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7537 nv = 96 ne = 84 npr = 48411 no. pairs analyzed = 48411 no. exposed pairs = 3173 no. arc points = 21536 no. surface atoms = 1071 nbur = 1340 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 523 mr = 4125 m= 1 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2017 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8746 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3914858E-09 2.9747929E-08 midg,1,midg; midg,igrid,midg 3.1860498E-08 -7.7453475E-09 1,midg,midg; igrid,midg,midg 7.3548598E-08 -6.3640535E-08 gauss-seidel spectral radius is 0.9889793 estimated iterations to convergence 78 setup time was (sec) 0.4800000 now iterating at: 12:21:36 rms-change max change #iterations 0.1915078 27.62134 at 10iterations 2.2175979E-02 3.116486 at 20iterations 2.6537410E-03 0.3762436 at 30iterations 3.3377297E-04 5.1563263E-02 at 40iterations 6.1447332E-05 8.9950562E-03 at 50iterations finished qdiffx linear iterations at : 12:21:39 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 6.1447332E-05 8.9950562E-03 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 12:21:39 3.042u 0.145s 0:03.46 91.9% 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 12:21:39 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2411 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: 2.059470 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): -14.32300 37.35800 ymin,ymax (A): -1.185000 44.82800 zmin,zma (A): -8.213000 43.64500 x,y,z range (A): 51.68100 46.01300 51.85800 scale (grids/A): 2.059470 object centre (A): 11.51750 21.82150 17.71600 number of atom coordinates read : 2411 total number of charged atoms : 2269 net assigned charge : 3.500025 assigned positive charge : 373.1932 centred at (gu) : 92.62825 94.42912 91.19511 assigned negative charge : -369.6935 centred at (gu) : 93.21331 94.62913 91.12319 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79474 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21536 grid for indexing accessible points = 1.400000 m= 31067 mr = 54226 m= 5853 mr = 22966 m= 482 mr = 3804 m= 13 mr = 216 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 35677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17984 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) : 0.6864901 object centre at (A) : 11.51750 21.82150 17.71600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4141416E-02 2.9764019E-03 midg,1,midg; midg,igrid,midg 3.0871771E-02 -2.8212497E-04 1,midg,midg; igrid,midg,midg 2.8506259E-02 -6.1075795E-02 gauss-seidel spectral radius is 0.9988077 estimated iterations to convergence 229 setup time was (sec) 0.8200000 now iterating at: 12:21:40 rms-change max change #iterations 4.874255 255.9266 at 10iterations 2.391083 83.66382 at 20iterations 1.179116 35.46978 at 30iterations 0.5790765 17.25441 at 40iterations 0.2854475 8.972870 at 50iterations 0.1404889 3.997629 at 60iterations 6.9125280E-02 2.083574 at 70iterations 3.4096435E-02 1.003204 at 80iterations 1.6753292E-02 0.4566572 at 90iterations 8.2719112E-03 0.2600002 at 100iterations 4.0752031E-03 0.1135406 at 110iterations 2.0202592E-03 5.7647705E-02 at 120iterations finished qdiffx linear iterations at : 12:21:46 total time elapsed so far: 7.040000 # loops : 120 mean,max change (kT/e) : 2.0202592E-03 5.7647705E-02 energy calculations done at 7.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.220000 DelPhi exited at 12:21:47 7.220u 0.175s 0:07.67 96.3% 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 12:21:47 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2411 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: 3.089205 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): -14.32300 37.35800 ymin,ymax (A): -1.185000 44.82800 zmin,zma (A): -8.213000 43.64500 x,y,z range (A): 51.68100 46.01300 51.85800 scale (grids/A): 3.089205 object centre (A): 11.51750 21.82150 17.71600 number of atom coordinates read : 2411 total number of charged atoms : 2269 net assigned charge : 3.500025 assigned positive charge : 373.1932 centred at (gu) : 93.94235 96.64359 91.79256 assigned negative charge : -369.6935 centred at (gu) : 94.81995 96.94366 91.68468 start vw surface at 0.1600000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 183230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21536 grid for indexing accessible points = 1.400000 m= 96104 mr = 131158 m= 39111 mr = 78530 m= 10859 mr = 31663 m= 1964 mr = 8207 m= 255 mr = 1313 m= 10 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.8799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.820000 number of dielectric boundary points 80495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 18152 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) : 2.059470 object centre at (A) : 11.51750 21.82150 17.71600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4805613 -0.2698258 midg,1,midg; midg,igrid,midg 0.2810392 -0.1177812 1,midg,midg; igrid,midg,midg 0.4906726 -0.7428722 gauss-seidel spectral radius is 0.9992951 estimated iterations to convergence 297 setup time was (sec) 2.090000 now iterating at: 12:21:49 rms-change max change #iterations 11.04854 515.8559 at 10iterations 6.537422 145.3424 at 20iterations 3.867984 80.89447 at 30iterations 2.281121 45.23497 at 40iterations 1.342502 24.65993 at 50iterations 0.7901886 14.29820 at 60iterations 0.4626394 8.498051 at 70iterations 0.2710533 4.505829 at 80iterations 0.1585589 2.937164 at 90iterations 9.2720203E-02 1.631012 at 100iterations 5.4205518E-02 0.9918212 at 110iterations 3.1720046E-02 0.6009054 at 120iterations 1.8554861E-02 0.3384018 at 130iterations 1.0853737E-02 0.1852551 at 140iterations 6.4175217E-03 0.1206245 at 150iterations 3.7940734E-03 7.8882217E-02 at 160iterations 2.2759407E-03 4.4483185E-02 at 170iterations 1.3973910E-03 2.8159142E-02 at 180iterations finished qdiffx linear iterations at : 12:21:59 total time elapsed so far: 11.43000 # loops : 180 mean,max change (kT/e) : 1.3973910E-03 2.8159142E-02 energy calculations done at 11.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.65000 DelPhi exited at 12:21:59 11.658u 0.176s 0:12.17 97.1% 0+0k 0+0io 0pf+0w