Mon Oct 10 19:32:20 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 Mon Oct 10 2011 at 19:32:20 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 = 2741 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: 0.5643090 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): -36.13100 18.25400 ymin,ymax (A): -13.96800 29.96500 zmin,zma (A): 10.83600 73.92200 x,y,z range (A): 54.38500 43.93300 63.08601 scale (grids/A): 0.5643090 object centre (A): -8.938500 7.998500 42.37900 number of atom coordinates read : 2741 total number of charged atoms : 2601 net assigned charge : 1.000028 assigned positive charge : 405.6168 centred at (gu) : 91.12924 90.33399 90.16993 assigned negative charge : -404.6176 centred at (gu) : 91.12644 90.24017 90.15861 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5638 nv = 96 ne = 84 npr = 55710 no. pairs analyzed = 55710 no. exposed pairs = 3397 no. arc points = 24576 no. surface atoms = 1151 nbur = 1590 mkacc time = 0.1600000 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 = 1.512000 m= 241 mr = 2934 m= 0 mr = 12 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3600000 number of dielectric boundary points 2933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2529 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7351 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1960970E-11 2.6341249E-10 midg,1,midg; midg,igrid,midg -9.1482949E-10 1.3107797E-09 1,midg,midg; igrid,midg,midg 6.7708124E-11 1.9999577E-10 gauss-seidel spectral radius is 0.9837812 estimated iterations to convergence 65 setup time was (sec) 0.6400000 now iterating at: 19:32:21 rms-change max change #iterations 8.0106705E-02 14.71941 at 10iterations 5.9462870E-03 0.9071736 at 20iterations 4.5810107E-04 7.7590942E-02 at 30iterations 4.9950741E-05 1.1657715E-02 at 40iterations 9.4624911E-06 2.4719238E-03 at 50iterations finished qdiffx linear iterations at : 19:32:24 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 9.4624911E-06 2.4719238E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 19:32:25 4.179u 0.264s 0:05.06 87.5% 0+0k 0+0io 4pf+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 Mon Oct 10 2011 at 19:32:25 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 = 2741 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: 1.692927 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): -36.13100 18.25400 ymin,ymax (A): -13.96800 29.96500 zmin,zma (A): 10.83600 73.92200 x,y,z range (A): 54.38500 43.93300 63.08601 scale (grids/A): 1.692927 object centre (A): -8.938500 7.998500 42.37900 number of atom coordinates read : 2741 total number of charged atoms : 2601 net assigned charge : 1.000028 assigned positive charge : 405.6168 centred at (gu) : 93.38737 91.00155 90.50958 assigned negative charge : -404.6176 centred at (gu) : 93.37908 90.72041 90.47563 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 61961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24576 grid for indexing accessible points = 1.400000 m= 19068 mr = 41604 m= 2132 mr = 13426 m= 46 mr = 1107 m= 0 mr = 7 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2737 time to turn everything in is 0.5700000 number of dielectric boundary points 27063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 241 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 20073 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) : 0.5643090 object centre at (A) : -8.938500 7.998500 42.37900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3725454E-02 4.3679313E-03 midg,1,midg; midg,igrid,midg -2.5295469E-03 5.8526462E-03 1,midg,midg; igrid,midg,midg 4.5001116E-03 -1.8556619E-03 gauss-seidel spectral radius is 0.9982914 estimated iterations to convergence 192 setup time was (sec) 0.8600000 now iterating at: 19:32:26 rms-change max change #iterations 3.402614 151.0638 at 10iterations 1.450548 57.14774 at 20iterations 0.6184026 23.98826 at 30iterations 0.2653921 8.705887 at 40iterations 0.1136412 4.309181 at 50iterations 4.8575401E-02 1.815542 at 60iterations 2.0697370E-02 0.7482128 at 70iterations 8.8788290E-03 0.3064175 at 80iterations 3.8097731E-03 0.1362486 at 90iterations 1.6315783E-03 5.6686401E-02 at 100iterations 7.0402096E-04 2.5788307E-02 at 110iterations 3.0404711E-04 1.1352539E-02 at 120iterations finished qdiffx linear iterations at : 19:32:34 total time elapsed so far: 9.250000 # loops : 120 mean,max change (kT/e) : 3.0404711E-04 1.1352539E-02 energy calculations done at 9.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.430000 DelPhi exited at 19:32:35 9.434u 0.300s 0:10.25 94.9% 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 Mon Oct 10 2011 at 19:32:35 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 = 2741 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: 2.539390 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): -36.13100 18.25400 ymin,ymax (A): -13.96800 29.96500 zmin,zma (A): 10.83600 73.92200 x,y,z range (A): 54.38500 43.93300 63.08601 scale (grids/A): 2.539390 object centre (A): -8.938500 7.998500 42.37900 number of atom coordinates read : 2741 total number of charged atoms : 2601 net assigned charge : 1.000028 assigned positive charge : 405.6168 centred at (gu) : 95.08084 91.50212 90.76426 assigned negative charge : -404.6176 centred at (gu) : 95.06865 91.08052 90.71330 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 143957 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24576 grid for indexing accessible points = 1.400000 m= 65494 mr = 102113 m= 19444 mr = 52040 m= 3372 mr = 14878 m= 281 mr = 2340 m= 5 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.7600001 no. cavity mid-points inaccessible to solvent = 9024 time to turn everything in is 1.350000 number of dielectric boundary points 61037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 20798 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) : 1.692927 object centre at (A) : -8.938500 7.998500 42.37900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2425538 4.2064365E-02 midg,1,midg; midg,igrid,midg -3.2490775E-02 5.0502669E-02 1,midg,midg; igrid,midg,midg 4.9641654E-02 0.1208230 gauss-seidel spectral radius is 0.9991663 estimated iterations to convergence 274 setup time was (sec) 1.660000 now iterating at: 19:32:37 rms-change max change #iterations 8.562716 293.7875 at 10iterations 4.834221 121.6310 at 20iterations 2.708242 62.08418 at 30iterations 1.510349 32.69392 at 40iterations 0.8429102 18.50616 at 50iterations 0.4700146 10.22401 at 60iterations 0.2616373 6.064097 at 70iterations 0.1452969 3.228600 at 80iterations 8.0725029E-02 1.646763 at 90iterations 4.4908796E-02 1.076496 at 100iterations 2.4893831E-02 0.5277596 at 110iterations 1.3803340E-02 0.3017359 at 120iterations 7.6857465E-03 0.1673069 at 130iterations 4.2520748E-03 9.4067097E-02 at 140iterations 2.3675561E-03 4.9775124E-02 at 150iterations 1.3193937E-03 2.9210567E-02 at 160iterations 7.3610066E-04 1.5813351E-02 at 170iterations 4.1351479E-04 9.3189478E-03 at 180iterations finished qdiffx linear iterations at : 19:32:51 total time elapsed so far: 15.34000 # loops : 180 mean,max change (kT/e) : 4.1351479E-04 9.3189478E-03 energy calculations done at 15.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.52000 DelPhi exited at 19:32:52 15.523u 0.327s 0:17.54 90.3% 0+0k 0+0io 0pf+0w