Sun Oct 9 12:21:56 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 12:21:56 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 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: 0.6924184 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): -14.37900 37.03500 ymin,ymax (A): 0.8270000 44.26400 zmin,zma (A): -6.091000 43.86900 x,y,z range (A): 51.41400 43.43700 49.96000 scale (grids/A): 0.6924184 object centre (A): 11.32800 22.54550 18.88900 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 372.6131 centred at (gu) : 91.11340 91.14001 89.70303 assigned negative charge : -369.1135 centred at (gu) : 91.29726 91.20120 89.66603 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7521 nv = 96 ne = 84 npr = 48952 no. pairs analyzed = 48952 no. exposed pairs = 2994 no. arc points = 20747 no. surface atoms = 1005 nbur = 1411 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 495 mr = 4155 m= 1 mr = 94 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 3768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1932 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8697421E-09 3.5069732E-08 midg,1,midg; midg,igrid,midg 3.7628027E-08 -4.8841926E-09 1,midg,midg; igrid,midg,midg 7.7397537E-08 -7.0306072E-08 gauss-seidel spectral radius is 0.9891625 estimated iterations to convergence 78 setup time was (sec) 0.5200000 now iterating at: 12:21:56 rms-change max change #iterations 0.2031814 27.50595 at 10iterations 2.3894420E-02 3.065941 at 20iterations 2.8857209E-03 0.3672142 at 30iterations 3.9522286E-04 5.1422119E-02 at 40iterations 6.9857866E-05 1.0848999E-02 at 50iterations finished qdiffx linear iterations at : 12:21:59 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 6.9857866E-05 1.0848999E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 12:22:00 3.382u 0.222s 0:03.89 92.5% 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 Sun Oct 9 2011 at 12:22:00 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 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: 2.077255 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): -14.37900 37.03500 ymin,ymax (A): 0.8270000 44.26400 zmin,zma (A): -6.091000 43.86900 x,y,z range (A): 51.41400 43.43700 49.96000 scale (grids/A): 2.077255 object centre (A): 11.32800 22.54550 18.88900 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 372.6131 centred at (gu) : 93.33954 93.41969 89.10865 assigned negative charge : -369.1135 centred at (gu) : 93.89171 93.60342 88.99786 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80184 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20747 grid for indexing accessible points = 1.400000 m= 31372 mr = 55592 m= 6265 mr = 23530 m= 592 mr = 4164 m= 22 mr = 298 m= 0 mr = 1 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 34850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 18056 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) : 0.6924184 object centre at (A) : 11.32800 22.54550 18.88900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3958167E-02 2.1153938E-02 midg,1,midg; midg,igrid,midg 3.7506420E-02 1.1542046E-03 1,midg,midg; igrid,midg,midg 2.2221029E-02 -6.5657876E-02 gauss-seidel spectral radius is 0.9988212 estimated iterations to convergence 231 setup time was (sec) 0.9100000 now iterating at: 12:22:01 rms-change max change #iterations 4.924345 211.9352 at 10iterations 2.418844 77.60297 at 20iterations 1.202623 36.66634 at 30iterations 0.5938567 19.11509 at 40iterations 0.2940190 8.735846 at 50iterations 0.1451026 4.419963 at 60iterations 7.2038390E-02 2.322819 at 70iterations 3.5568152E-02 1.072498 at 80iterations 1.7600050E-02 0.5240860 at 90iterations 8.7333918E-03 0.2541313 at 100iterations 4.3452373E-03 0.1365547 at 110iterations 2.1731909E-03 6.5613449E-02 at 120iterations finished qdiffx linear iterations at : 12:22:07 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 2.1731909E-03 6.5613449E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 12:22:08 7.902u 0.244s 0:08.47 96.1% 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 12:22:08 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 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: 3.115883 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): -14.37900 37.03500 ymin,ymax (A): 0.8270000 44.26400 zmin,zma (A): -6.091000 43.86900 x,y,z range (A): 51.41400 43.43700 49.96000 scale (grids/A): 3.115883 object centre (A): 11.32800 22.54550 18.88900 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 372.6131 centred at (gu) : 95.00921 95.12938 88.66288 assigned negative charge : -369.1135 centred at (gu) : 95.83750 95.40497 88.49673 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 185121 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20747 grid for indexing accessible points = 1.400000 m= 97611 mr = 134592 m= 39996 mr = 80179 m= 11792 mr = 32875 m= 2501 mr = 9145 m= 310 mr = 1807 m= 19 mr = 166 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.810000 number of dielectric boundary points 78582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 18192 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) : 2.077255 object centre at (A) : 11.32800 22.54550 18.88900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2148577 9.1564842E-02 midg,1,midg; midg,igrid,midg 0.3270922 -0.1110739 1,midg,midg; igrid,midg,midg 0.3891874 -0.6463246 gauss-seidel spectral radius is 0.9993001 estimated iterations to convergence 298 setup time was (sec) 2.090000 now iterating at: 12:22:10 rms-change max change #iterations 11.12558 412.9722 at 10iterations 6.612790 139.9980 at 20iterations 3.916377 88.68481 at 30iterations 2.316560 46.10270 at 40iterations 1.367381 25.45645 at 50iterations 0.8038307 17.01490 at 60iterations 0.4730513 8.538229 at 70iterations 0.2774077 5.010994 at 80iterations 0.1626469 2.868927 at 90iterations 9.5472611E-02 1.730278 at 100iterations 5.5910744E-02 0.9348583 at 110iterations 3.2840803E-02 0.5249023 at 120iterations 1.9206129E-02 0.3148499 at 130iterations 1.1294715E-02 0.1956711 at 140iterations 6.6624330E-03 0.1078606 at 150iterations 3.9458401E-03 6.9015503E-02 at 160iterations 2.3642681E-03 4.5001984E-02 at 170iterations 1.4463392E-03 3.0765533E-02 at 180iterations finished qdiffx linear iterations at : 12:22:20 total time elapsed so far: 11.55000 # loops : 180 mean,max change (kT/e) : 1.4463392E-03 3.0765533E-02 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.73000 DelPhi exited at 12:22:20 11.731u 0.177s 0:12.22 97.3% 0+0k 0+0io 0pf+0w