Sat Oct 8 17:25:32 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 Sat Oct 8 2011 at 17:25:32 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3742 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5439516 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): -1.662000 60.34600 ymin,ymax (A): -18.56100 44.44000 zmin,zma (A): -6.473000 58.97400 x,y,z range (A): 62.00800 63.00100 65.44701 scale (grids/A): 0.5439516 object centre (A): 29.34200 12.93950 26.25050 number of atom coordinates read : 3742 total number of charged atoms : 3592 net assigned charge : -8.999968 assigned positive charge : 569.4443 centred at (gu) : 88.76581 86.80066 90.74701 assigned negative charge : -578.4468 centred at (gu) : 88.82546 86.80556 90.77151 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7180 nv = 96 ne = 84 npr = 75114 no. pairs analyzed = 75114 no. exposed pairs = 4880 no. arc points = 34823 no. surface atoms = 1629 nbur = 2113 mkacc time = 0.2100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 301 mr = 3629 m= 3 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 3844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3500 ## 442 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 9484 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7142949E-10 -8.5190804E-10 midg,1,midg; midg,igrid,midg -1.0433098E-09 -2.5938074E-10 1,midg,midg; igrid,midg,midg -5.6671258E-11 -7.3153494E-10 gauss-seidel spectral radius is 0.9826374 estimated iterations to convergence 63 setup time was (sec) 0.7300000 now iterating at: 17:25:33 rms-change max change #iterations 8.3286494E-02 13.81869 at 10iterations 5.6894599E-03 0.8539295 at 20iterations 5.4130616E-04 9.2411041E-02 at 30iterations 1.1581950E-04 2.2397995E-02 at 40iterations 3.3190856E-05 6.2255859E-03 at 50iterations finished qdiffx linear iterations at : 17:25:36 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 3.3190856E-05 6.2255859E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 17:25:37 4.319u 0.227s 0:04.81 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 Sat Oct 8 2011 at 17:25:37 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3742 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: 1.631855 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): -1.662000 60.34600 ymin,ymax (A): -18.56100 44.44000 zmin,zma (A): -6.473000 58.97400 x,y,z range (A): 62.00800 63.00100 65.44701 scale (grids/A): 1.631855 object centre (A): 29.34200 12.93950 26.25050 number of atom coordinates read : 3742 total number of charged atoms : 3592 net assigned charge : -8.999968 assigned positive charge : 569.4443 centred at (gu) : 86.29642 80.40095 92.24014 assigned negative charge : -578.4468 centred at (gu) : 86.47617 80.41666 92.31413 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 79752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34823 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 24593 mr = 53622 m= 2576 mr = 16409 m= 66 mr = 1181 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 35768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 383 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 27500 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) : 0.5439516 object centre at (A) : 29.34200 12.93950 26.25050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8282938E-04 -1.0275798E-02 midg,1,midg; midg,igrid,midg -2.6247891E-02 -6.2800827E-03 1,midg,midg; igrid,midg,midg -1.0597192E-02 -2.6114609E-02 gauss-seidel spectral radius is 0.9982559 estimated iterations to convergence 190 setup time was (sec) 1.030000 now iterating at: 17:25:38 rms-change max change #iterations 3.850432 173.9924 at 10iterations 1.629832 57.76462 at 20iterations 0.6893600 22.95129 at 30iterations 0.2917644 9.436659 at 40iterations 0.1242793 4.344326 at 50iterations 5.2622553E-02 1.736748 at 60iterations 2.2408852E-02 0.8025987 at 70iterations 9.5180627E-03 0.3372211 at 80iterations 4.0509212E-03 0.1336861 at 90iterations 1.7338080E-03 5.8074951E-02 at 100iterations 7.4781087E-04 2.5238037E-02 at 110iterations 3.2855608E-04 1.0967255E-02 at 120iterations finished qdiffx linear iterations at : 17:25:47 total time elapsed so far: 9.560000 # loops : 120 mean,max change (kT/e) : 3.2855608E-04 1.0967255E-02 energy calculations done at 9.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.740000 DelPhi exited at 17:25:47 9.741u 0.233s 0:10.26 97.1% 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 Sat Oct 8 2011 at 17:25:47 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3742 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: 2.447782 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): -1.662000 60.34600 ymin,ymax (A): -18.56100 44.44000 zmin,zma (A): -6.473000 58.97400 x,y,z range (A): 62.00800 63.00100 65.44701 scale (grids/A): 2.447782 object centre (A): 29.34200 12.93950 26.25050 number of atom coordinates read : 3742 total number of charged atoms : 3592 net assigned charge : -8.999968 assigned positive charge : 569.4443 centred at (gu) : 84.44431 75.60110 93.36001 assigned negative charge : -578.4468 centred at (gu) : 84.71397 75.62492 93.47097 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 184982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34823 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 85412 mr = 131405 m= 24197 mr = 66552 m= 3921 mr = 17727 m= 240 mr = 2369 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.510000 number of dielectric boundary points 80638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 28698 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) : 1.631855 object centre at (A) : 29.34200 12.93950 26.25050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7933886E-02 5.8402058E-02 midg,1,midg; midg,igrid,midg -0.4035695 -9.4547696E-02 1,midg,midg; igrid,midg,midg -0.1748976 -0.5147779 gauss-seidel spectral radius is 0.9991756 estimated iterations to convergence 275 setup time was (sec) 1.910000 now iterating at: 17:25:49 rms-change max change #iterations 9.954897 253.9541 at 10iterations 5.693170 147.0102 at 20iterations 3.237934 77.31910 at 30iterations 1.828736 39.47704 at 40iterations 1.029561 24.32132 at 50iterations 0.5775948 12.63302 at 60iterations 0.3238655 6.714480 at 70iterations 0.1815439 3.991431 at 80iterations 0.1014801 2.392684 at 90iterations 5.6686632E-02 1.381180 at 100iterations 3.1680450E-02 0.6384773 at 110iterations 1.7677208E-02 0.3345261 at 120iterations 9.8771648E-03 0.2045803 at 130iterations 5.5324510E-03 0.1018372 at 140iterations 3.0968243E-03 6.1072350E-02 at 150iterations 1.7423893E-03 3.4072876E-02 at 160iterations 9.8784314E-04 1.9491673E-02 at 170iterations 5.6738674E-04 1.1284828E-02 at 180iterations finished qdiffx linear iterations at : 17:26:04 total time elapsed so far: 16.31000 # loops : 180 mean,max change (kT/e) : 5.6738674E-04 1.1284828E-02 energy calculations done at 16.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.53000 DelPhi exited at 17:26:04 16.528u 0.322s 0:17.16 98.1% 0+0k 0+0io 0pf+0w