Mon Oct 10 19:36:14 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 Mon Oct 10 2011 at 19:36:14 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 = 2203 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: 0.6395516 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): -35.89600 2.145000 ymin,ymax (A): 31.91200 87.57600 zmin,zma (A): -24.56000 24.92100 x,y,z range (A): 38.04100 55.66400 49.48100 scale (grids/A): 0.6395516 object centre (A): -16.87550 59.74400 0.1805000 number of atom coordinates read : 2203 total number of charged atoms : 2129 net assigned charge : -1.999997 assigned positive charge : 322.9585 centred at (gu) : 88.91989 91.92362 89.82018 assigned negative charge : -324.9589 centred at (gu) : 88.88624 91.89174 89.85903 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6109 nv = 96 ne = 84 npr = 44374 no. pairs analyzed = 44374 no. exposed pairs = 2863 no. arc points = 20222 no. surface atoms = 966 nbur = 1237 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 392 mr = 3288 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2800000 number of dielectric boundary points 3152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1930 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7406 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6065061E-10 -6.3884724E-09 midg,1,midg; midg,igrid,midg -3.9795149E-09 3.4078995E-10 1,midg,midg; igrid,midg,midg -7.7330347E-09 2.2905373E-10 gauss-seidel spectral radius is 0.9873030 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 19:36:15 rms-change max change #iterations 0.1314918 23.54102 at 10iterations 1.2833638E-02 1.883530 at 20iterations 1.2415659E-03 0.1978760 at 30iterations 1.2577015E-04 1.9012451E-02 at 40iterations 1.2570277E-05 1.6250610E-03 at 50iterations finished qdiffx linear iterations at : 19:36:17 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.2570277E-05 1.6250610E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 19:36:18 3.532u 0.195s 0:04.39 84.7% 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 19:36:18 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 = 2203 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: 1.918655 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): -35.89600 2.145000 ymin,ymax (A): 31.91200 87.57600 zmin,zma (A): -24.56000 24.92100 x,y,z range (A): 38.04100 55.66400 49.48100 scale (grids/A): 1.918655 object centre (A): -16.87550 59.74400 0.1805000 number of atom coordinates read : 2203 total number of charged atoms : 2129 net assigned charge : -1.999997 assigned positive charge : 322.9585 centred at (gu) : 86.75958 95.77035 89.46037 assigned negative charge : -324.9589 centred at (gu) : 86.65861 95.67513 89.57690 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 65849 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20222 grid for indexing accessible points = 1.400000 m= 24609 mr = 45144 m= 4669 mr = 18050 m= 362 mr = 3059 m= 5 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 665 time to turn everything in is 0.5400000 number of dielectric boundary points 29072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 16789 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) : 0.6395516 object centre at (A) : -16.87550 59.74400 0.1805000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6598227E-03 -2.6248859E-02 midg,1,midg; midg,igrid,midg 7.2229877E-03 -4.0722039E-02 1,midg,midg; igrid,midg,midg -1.4760970E-02 1.2850137E-02 gauss-seidel spectral radius is 0.9986194 estimated iterations to convergence 213 setup time was (sec) 0.8500000 now iterating at: 19:36:19 rms-change max change #iterations 3.880398 156.4003 at 10iterations 1.808055 67.80537 at 20iterations 0.8445852 29.43407 at 30iterations 0.3945378 15.28287 at 40iterations 0.1840332 6.439117 at 50iterations 8.5829020E-02 3.316809 at 60iterations 4.0185325E-02 1.366577 at 70iterations 1.8689767E-02 0.5913658 at 80iterations 8.7350821E-03 0.3059149 at 90iterations 4.0695239E-03 0.1403062 at 100iterations 1.9013485E-03 6.1985493E-02 at 110iterations 8.9275732E-04 2.9637456E-02 at 120iterations finished qdiffx linear iterations at : 19:36:26 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 8.9275732E-04 2.9637456E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 19:36:27 7.959u 0.215s 0:08.63 94.5% 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 Mon Oct 10 2011 at 19:36:27 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 = 2203 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: 2.877982 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): -35.89600 2.145000 ymin,ymax (A): 31.91200 87.57600 zmin,zma (A): -24.56000 24.92100 x,y,z range (A): 38.04100 55.66400 49.48100 scale (grids/A): 2.877982 object centre (A): -16.87550 59.74400 0.1805000 number of atom coordinates read : 2203 total number of charged atoms : 2129 net assigned charge : -1.999997 assigned positive charge : 322.9585 centred at (gu) : 85.13927 98.65549 89.19035 assigned negative charge : -324.9589 centred at (gu) : 84.98794 98.51268 89.36552 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 152340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20222 grid for indexing accessible points = 1.400000 m= 77435 mr = 109713 m= 30390 mr = 62856 m= 8553 mr = 24453 m= 1570 mr = 6653 m= 126 mr = 1151 m= 0 mr = 67 time to grow re-entrant surface = 0.8000001 no. cavity mid-points inaccessible to solvent = 2075 time to turn everything in is 1.360000 number of dielectric boundary points 65521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 17032 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) : 1.918655 object centre at (A) : -16.87550 59.74400 0.1805000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1506191E-02 -0.2176889 midg,1,midg; midg,igrid,midg 0.2820045 -0.8666896 1,midg,midg; igrid,midg,midg -0.2017761 0.1602831 gauss-seidel spectral radius is 0.9992522 estimated iterations to convergence 289 setup time was (sec) 1.680000 now iterating at: 19:36:29 rms-change max change #iterations 9.088920 340.9070 at 10iterations 5.272795 116.6458 at 20iterations 3.038660 62.72465 at 30iterations 1.757850 36.77927 at 40iterations 1.008133 19.50139 at 50iterations 0.5824356 10.81058 at 60iterations 0.3341871 6.818768 at 70iterations 0.1922281 3.475063 at 80iterations 0.1099798 2.033203 at 90iterations 6.3009724E-02 1.284850 at 100iterations 3.6144450E-02 0.7150631 at 110iterations 2.0783344E-02 0.3803961 at 120iterations 1.1891126E-02 0.2497463 at 130iterations 6.8166400E-03 0.1329899 at 140iterations 3.8976979E-03 7.2590828E-02 at 150iterations 2.2338794E-03 4.3863297E-02 at 160iterations 1.2789776E-03 2.3048401E-02 at 170iterations 7.3275378E-04 1.4080524E-02 at 180iterations finished qdiffx linear iterations at : 19:36:40 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 7.3275378E-04 1.4080524E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 19:36:41 13.088u 0.264s 0:13.71 97.3% 0+0k 0+0io 0pf+0w