Sun Oct 9 10:38:14 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 10:38:14 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 = 2210 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6160235 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): -1.627000 48.58800 ymin,ymax (A): -26.86100 30.92900 zmin,zma (A): -5.566000 47.48100 x,y,z range (A): 50.21500 57.79000 53.04700 scale (grids/A): 0.6160235 object centre (A): 23.48050 2.033999 20.95750 number of atom coordinates read : 2210 total number of charged atoms : 2073 net assigned charge : 2.500015 assigned positive charge : 320.1205 centred at (gu) : 90.33631 90.99552 91.23838 assigned negative charge : -317.6213 centred at (gu) : 90.37409 90.85801 91.23334 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5657 nv = 96 ne = 84 npr = 44218 no. pairs analyzed = 44218 no. exposed pairs = 3005 no. arc points = 21386 no. surface atoms = 999 nbur = 1211 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 2844 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2800000 number of dielectric boundary points 3069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2126 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6914 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1307371E-09 2.5559121E-09 midg,1,midg; midg,igrid,midg -4.0124890E-09 1.0322502E-08 1,midg,midg; igrid,midg,midg 3.2776941E-09 -1.4052118E-10 gauss-seidel spectral radius is 0.9863303 estimated iterations to convergence 70 setup time was (sec) 0.5000000 now iterating at: 10:38:15 rms-change max change #iterations 0.1070686 17.26683 at 10iterations 9.6872253E-03 1.729459 at 20iterations 8.4934063E-04 0.1430588 at 30iterations 7.7716890E-05 1.4718056E-02 at 40iterations 6.9981688E-06 1.1730194E-03 at 50iterations finished qdiffx linear iterations at : 10:38:17 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 6.9981688E-06 1.1730194E-03 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 10:38:18 3.056u 0.137s 0:03.56 89.3% 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 10:38:18 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 = 2210 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.848071 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): -1.627000 48.58800 ymin,ymax (A): -26.86100 30.92900 zmin,zma (A): -5.566000 47.48100 x,y,z range (A): 50.21500 57.79000 53.04700 scale (grids/A): 1.848071 object centre (A): 23.48050 2.033999 20.95750 number of atom coordinates read : 2210 total number of charged atoms : 2073 net assigned charge : 2.500015 assigned positive charge : 320.1205 centred at (gu) : 91.00845 92.98623 93.71496 assigned negative charge : -317.6213 centred at (gu) : 91.12241 92.57414 93.70011 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 60946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21386 grid for indexing accessible points = 1.400000 m= 20256 mr = 39859 m= 3230 mr = 14114 m= 205 mr = 2048 m= 5 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 28556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 16241 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) : 0.6160235 object centre at (A) : 23.48050 2.033999 20.95750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4095869E-03 3.2361217E-02 midg,1,midg; midg,igrid,midg -1.3880910E-03 2.6916007E-02 1,midg,midg; igrid,midg,midg -9.6159456E-03 -1.5451666E-02 gauss-seidel spectral radius is 0.9985218 estimated iterations to convergence 206 setup time was (sec) 0.6900000 now iterating at: 10:38:19 rms-change max change #iterations 3.620029 184.5610 at 10iterations 1.635720 68.32543 at 20iterations 0.7440318 29.21317 at 30iterations 0.3365206 12.29018 at 40iterations 0.1526682 5.431707 at 50iterations 6.9600016E-02 2.336888 at 60iterations 3.1438995E-02 1.057806 at 70iterations 1.4243060E-02 0.4951420 at 80iterations 6.4682201E-03 0.2254877 at 90iterations 2.9470192E-03 0.1155663 at 100iterations 1.3291261E-03 4.6062469E-02 at 110iterations 6.0635450E-04 2.1530151E-02 at 120iterations finished qdiffx linear iterations at : 10:38:24 total time elapsed so far: 6.580000 # loops : 120 mean,max change (kT/e) : 6.0635450E-04 2.1530151E-02 energy calculations done at 6.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.740000 DelPhi exited at 10:38:25 6.746u 0.166s 0:07.20 95.8% 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 10:38:25 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 = 2210 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: 2.772106 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): -1.627000 48.58800 ymin,ymax (A): -26.86100 30.92900 zmin,zma (A): -5.566000 47.48100 x,y,z range (A): 50.21500 57.79000 53.04700 scale (grids/A): 2.772106 object centre (A): 23.48050 2.033999 20.95750 number of atom coordinates read : 2210 total number of charged atoms : 2073 net assigned charge : 2.500015 assigned positive charge : 320.1205 centred at (gu) : 91.51259 94.47934 95.57227 assigned negative charge : -317.6213 centred at (gu) : 91.68374 93.86124 95.55035 start vw surface at 0.1400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 141190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21386 grid for indexing accessible points = 1.400000 m= 65847 mr = 97744 m= 23118 mr = 51919 m= 5754 mr = 17977 m= 834 mr = 4343 m= 50 mr = 573 m= 0 mr = 13 time to grow re-entrant surface = 0.5899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 64224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 16584 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) : 1.848071 object centre at (A) : 23.48050 2.033999 20.95750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1524285 0.3996721 midg,1,midg; midg,igrid,midg -3.8974274E-02 0.2421234 1,midg,midg; igrid,midg,midg -0.1504681 -0.1929784 gauss-seidel spectral radius is 0.9992251 estimated iterations to convergence 284 setup time was (sec) 1.340000 now iterating at: 10:38:27 rms-change max change #iterations 8.534429 335.3936 at 10iterations 4.893201 125.8188 at 20iterations 2.798131 60.89647 at 30iterations 1.589860 39.75155 at 40iterations 0.9018441 18.25942 at 50iterations 0.5137449 11.12764 at 60iterations 0.2905896 5.666203 at 70iterations 0.1644792 3.403900 at 80iterations 9.3262807E-02 1.910591 at 90iterations 5.2943163E-02 1.065853 at 100iterations 2.9915344E-02 0.6230593 at 110iterations 1.6944109E-02 0.3434315 at 120iterations 9.5985634E-03 0.2020082 at 130iterations 5.4331683E-03 0.1143875 at 140iterations 3.0882733E-03 6.5856934E-02 at 150iterations 1.7475465E-03 3.6082268E-02 at 160iterations 9.8991150E-04 1.8962860E-02 at 170iterations 5.6203955E-04 1.1369705E-02 at 180iterations finished qdiffx linear iterations at : 10:38:36 total time elapsed so far: 10.48000 # loops : 180 mean,max change (kT/e) : 5.6203955E-04 1.1369705E-02 energy calculations done at 10.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.64000 DelPhi exited at 10:38:36 10.646u 0.166s 0:11.25 96.0% 0+0k 0+0io 0pf+0w