Tue Oct 11 03:22:51 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 Tue Oct 11 2011 at 03:22:51 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3395 !!! WARNING: HIR 502 has a net charge of 0.5140 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: 0.5482067 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): -34.44700 22.18500 ymin,ymax (A): -4.805000 60.13400 zmin,zma (A): -7.579000 47.37300 x,y,z range (A): 56.63200 64.93900 54.95200 scale (grids/A): 0.5482067 object centre (A): -6.131000 27.66450 19.89700 number of atom coordinates read : 3395 total number of charged atoms : 3234 net assigned charge : 5.014029 assigned positive charge : 506.9742 centred at (gu) : 90.94611 87.62917 88.97829 assigned negative charge : -501.9620 centred at (gu) : 91.07966 87.35293 88.87714 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6920 nv = 96 ne = 84 npr = 64042 no. pairs analyzed = 64042 no. exposed pairs = 5000 no. arc points = 35968 no. surface atoms = 1649 nbur = 1746 mkacc time = 0.1100000 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 = 1.540000 m= 314 mr = 3108 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4104 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3551 ## 425 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8805 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2684923E-10 9.5394248E-10 midg,1,midg; midg,igrid,midg -3.4622105E-09 1.4371904E-09 1,midg,midg; igrid,midg,midg 1.1718951E-09 -8.5768209E-10 gauss-seidel spectral radius is 0.9828966 estimated iterations to convergence 63 setup time was (sec) 0.4100000 now iterating at: 03:22:51 rms-change max change #iterations 7.7296257E-02 12.25707 at 10iterations 5.2571190E-03 0.7618923 at 20iterations 4.3342373E-04 7.0861816E-02 at 30iterations 6.0769649E-05 1.0314941E-02 at 40iterations 1.2332749E-05 1.7814636E-03 at 50iterations finished qdiffx linear iterations at : 03:22:54 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.2332749E-05 1.7814636E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 03:22:55 3.396u 0.179s 0:03.86 92.2% 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 Tue Oct 11 2011 at 03:22:55 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3395 !!! WARNING: HIR 502 has a net charge of 0.5140 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: 1.644620 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): -34.44700 22.18500 ymin,ymax (A): -4.805000 60.13400 zmin,zma (A): -7.579000 47.37300 x,y,z range (A): 56.63200 64.93900 54.95200 scale (grids/A): 1.644620 object centre (A): -6.131000 27.66450 19.89700 number of atom coordinates read : 3395 total number of charged atoms : 3234 net assigned charge : 5.014029 assigned positive charge : 506.9742 centred at (gu) : 92.83736 82.88635 86.93431 assigned negative charge : -501.9620 centred at (gu) : 93.23844 82.05884 86.63107 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35968 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24306 mr = 46644 m= 3126 mr = 15829 m= 108 mr = 1504 m= 0 mr = 9 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 38152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 374 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 24816 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) : 0.5482067 object centre at (A) : -6.131000 27.66450 19.89700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8367156E-03 3.0027945E-03 midg,1,midg; midg,igrid,midg 2.3135968E-02 5.6451716E-02 1,midg,midg; igrid,midg,midg -6.2020468E-03 -2.6848970E-03 gauss-seidel spectral radius is 0.9982833 estimated iterations to convergence 192 setup time was (sec) 0.5800000 now iterating at: 03:22:55 rms-change max change #iterations 3.644491 168.3154 at 10iterations 1.544517 55.98234 at 20iterations 0.6566985 24.45404 at 30iterations 0.2790196 9.218335 at 40iterations 0.1186057 4.040329 at 50iterations 5.0765745E-02 1.616077 at 60iterations 2.1643128E-02 0.6871557 at 70iterations 9.2193084E-03 0.3188133 at 80iterations 3.9355545E-03 0.1323929 at 90iterations 1.6973387E-03 5.7295799E-02 at 100iterations 7.2622712E-04 2.6721954E-02 at 110iterations 3.1173954E-04 1.1043549E-02 at 120iterations finished qdiffx linear iterations at : 03:23:02 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 3.1173954E-04 1.1043549E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 03:23:03 7.760u 0.191s 0:08.38 94.8% 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 Tue Oct 11 2011 at 03:23:03 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3395 !!! WARNING: HIR 502 has a net charge of 0.5140 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: 2.466930 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): -34.44700 22.18500 ymin,ymax (A): -4.805000 60.13400 zmin,zma (A): -7.579000 47.37300 x,y,z range (A): 56.63200 64.93900 54.95200 scale (grids/A): 2.466930 object centre (A): -6.131000 27.66450 19.89700 number of atom coordinates read : 3395 total number of charged atoms : 3234 net assigned charge : 5.014029 assigned positive charge : 506.9742 centred at (gu) : 94.25557 79.32914 85.40115 assigned negative charge : -501.9620 centred at (gu) : 94.85769 78.08792 84.94650 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 172850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35968 grid for indexing accessible points = 1.400000 m= 79862 mr = 115442 m= 26057 mr = 60310 m= 4921 mr = 18928 m= 357 mr = 3082 m= 4 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9100000 number of dielectric boundary points 86153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 25832 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) : 1.644620 object centre at (A) : -6.131000 27.66450 19.89700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1165298 3.9163504E-02 midg,1,midg; midg,igrid,midg 0.4934891 0.9826350 1,midg,midg; igrid,midg,midg -0.1283995 2.7750507E-02 gauss-seidel spectral radius is 0.9991952 estimated iterations to convergence 278 setup time was (sec) 1.160000 now iterating at: 03:23:04 rms-change max change #iterations 9.755520 291.3344 at 10iterations 5.720946 154.6070 at 20iterations 3.312916 83.62192 at 30iterations 1.902462 44.30616 at 40iterations 1.087013 23.27839 at 50iterations 0.6173177 13.53572 at 60iterations 0.3508902 7.652578 at 70iterations 0.1980994 4.167900 at 80iterations 0.1116639 2.201294 at 90iterations 6.2988274E-02 1.274046 at 100iterations 3.5488218E-02 0.7417055 at 110iterations 1.9912517E-02 0.4109039 at 120iterations 1.1200455E-02 0.2316132 at 130iterations 6.2990035E-03 0.1355906 at 140iterations 3.5286285E-03 6.9206238E-02 at 150iterations 1.9837907E-03 4.4888496E-02 at 160iterations 1.1135555E-03 2.1585464E-02 at 170iterations 6.2736613E-04 1.3058662E-02 at 180iterations finished qdiffx linear iterations at : 03:23:16 total time elapsed so far: 12.54000 # loops : 180 mean,max change (kT/e) : 6.2736613E-04 1.3058662E-02 energy calculations done at 12.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.67000 DelPhi exited at 03:23:16 12.675u 0.192s 0:13.19 97.4% 0+0k 0+0io 0pf+0w