Sun Oct 9 10:38:33 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 10:38:33 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 = 3221 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: 0.5403355 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): 39.40800 104.3670 ymin,ymax (A): 3.341000 69.22600 zmin,zma (A): -13.16200 39.78000 x,y,z range (A): 64.95900 65.88499 52.94200 scale (grids/A): 0.5403355 object centre (A): 71.88750 36.28350 13.30900 number of atom coordinates read : 3221 total number of charged atoms : 3072 net assigned charge : -4.999968 assigned positive charge : 472.5394 centred at (gu) : 90.76540 90.92319 89.69360 assigned negative charge : -477.5413 centred at (gu) : 90.60881 90.90195 89.56687 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6323 nv = 96 ne = 84 npr = 62046 no. pairs analyzed = 62046 no. exposed pairs = 4818 no. arc points = 34486 no. surface atoms = 1588 nbur = 1633 mkacc time = 0.1400000 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= 283 mr = 2832 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3374 ## 423 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8261 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0761078E-09 4.2906637E-10 midg,1,midg; midg,igrid,midg -3.0048311E-10 -1.6359251E-10 1,midg,midg; igrid,midg,midg -9.6938024E-10 7.6924445E-10 gauss-seidel spectral radius is 0.9823830 estimated iterations to convergence 62 setup time was (sec) 0.5800000 now iterating at: 10:38:34 rms-change max change #iterations 6.8424627E-02 10.74505 at 10iterations 4.4787773E-03 0.8289185 at 20iterations 3.0367202E-04 5.4853439E-02 at 30iterations 2.4079778E-05 4.7464371E-03 at 40iterations 3.0257627E-06 5.6171417E-04 at 50iterations finished qdiffx linear iterations at : 10:38:37 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.0257627E-06 5.6171417E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 10:38:37 3.487u 0.183s 0:03.96 92.4% 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 10:38:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 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: 1.621006 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): 39.40800 104.3670 ymin,ymax (A): 3.341000 69.22600 zmin,zma (A): -13.16200 39.78000 x,y,z range (A): 64.95900 65.88499 52.94200 scale (grids/A): 1.621006 object centre (A): 71.88750 36.28350 13.30900 number of atom coordinates read : 3221 total number of charged atoms : 3072 net assigned charge : -4.999968 assigned positive charge : 472.5394 centred at (gu) : 92.29508 92.76807 89.07985 assigned negative charge : -477.5413 centred at (gu) : 91.82607 92.70567 88.70018 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70169 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34486 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19756 mr = 44119 m= 1891 mr = 11914 m= 52 mr = 721 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 68 time to turn everything in is 0.5400000 number of dielectric boundary points 35114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 330 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 23520 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) : 0.5403355 object centre at (A) : 71.88750 36.28350 13.30900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0842480E-03 1.1394266E-02 midg,1,midg; midg,igrid,midg -1.7068576E-02 -1.4638920E-02 1,midg,midg; igrid,midg,midg -2.4170805E-02 1.5139006E-02 gauss-seidel spectral radius is 0.9982090 estimated iterations to convergence 188 setup time was (sec) 0.8400000 now iterating at: 10:38:38 rms-change max change #iterations 3.381644 168.6339 at 10iterations 1.408548 54.65609 at 20iterations 0.5874075 23.85232 at 30iterations 0.2443324 8.908345 at 40iterations 0.1023780 3.591232 at 50iterations 4.2737812E-02 1.475002 at 60iterations 1.7894398E-02 0.6794889 at 70iterations 7.4967528E-03 0.2814903 at 80iterations 3.1244617E-03 0.1353321 at 90iterations 1.3116909E-03 4.6424866E-02 at 100iterations 5.5202405E-04 1.9455910E-02 at 110iterations 2.3059756E-04 8.3971024E-03 at 120iterations finished qdiffx linear iterations at : 10:38:46 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 2.3059756E-04 8.3971024E-03 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.440000 DelPhi exited at 10:38:46 8.438u 0.211s 0:08.92 96.8% 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 10:38:46 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 = 3221 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: 2.431510 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): 39.40800 104.3670 ymin,ymax (A): 3.341000 69.22600 zmin,zma (A): -13.16200 39.78000 x,y,z range (A): 64.95900 65.88499 52.94200 scale (grids/A): 2.431510 object centre (A): 71.88750 36.28350 13.30900 number of atom coordinates read : 3221 total number of charged atoms : 3072 net assigned charge : -4.999968 assigned positive charge : 472.5394 centred at (gu) : 93.44233 94.15179 88.61933 assigned negative charge : -477.5413 centred at (gu) : 92.73893 94.05840 88.05021 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 163391 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34486 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 68684 mr = 109665 m= 18149 mr = 50559 m= 2698 mr = 12190 m= 151 mr = 1424 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 267 time to turn everything in is 1.290000 number of dielectric boundary points 79183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 24550 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) : 1.621006 object centre at (A) : 71.88750 36.28350 13.30900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1297809 0.1762946 midg,1,midg; midg,igrid,midg -0.4197554 -0.2704789 1,midg,midg; igrid,midg,midg -0.2706826 0.3395376 gauss-seidel spectral radius is 0.9991568 estimated iterations to convergence 272 setup time was (sec) 1.620000 now iterating at: 10:38:48 rms-change max change #iterations 8.999973 330.3365 at 10iterations 5.133668 158.5562 at 20iterations 2.907183 69.91972 at 30iterations 1.639910 35.28967 at 40iterations 0.9204287 20.30864 at 50iterations 0.5129910 10.94557 at 60iterations 0.2858320 5.989194 at 70iterations 0.1587339 3.684087 at 80iterations 8.8021711E-02 1.935276 at 90iterations 4.8764259E-02 0.9625111 at 100iterations 2.7054779E-02 0.5589314 at 110iterations 1.4963747E-02 0.3098223 at 120iterations 8.2778223E-03 0.1733589 at 130iterations 4.5807329E-03 9.3860626E-02 at 140iterations 2.5313285E-03 5.2010536E-02 at 150iterations 1.3971855E-03 2.8053284E-02 at 160iterations 7.7594974E-04 1.5949249E-02 at 170iterations 4.2838248E-04 9.3841553E-03 at 180iterations finished qdiffx linear iterations at : 10:39:00 total time elapsed so far: 13.20000 # loops : 180 mean,max change (kT/e) : 4.2838248E-04 9.3841553E-03 energy calculations done at 13.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 10:39:00 13.391u 0.223s 0:13.90 97.9% 0+0k 0+0io 0pf+0w