Mon Oct 10 14:10:42 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 Mon Oct 10 2011 at 14:10:42 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3419 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: 0.5750933 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): -10.03000 43.15900 ymin,ymax (A): 6.634000 62.70900 zmin,zma (A): -3.710000 58.19300 x,y,z range (A): 53.18900 56.07500 61.90300 scale (grids/A): 0.5750933 object centre (A): 16.56450 34.67150 27.24150 number of atom coordinates read : 3419 total number of charged atoms : 3275 net assigned charge : -3.999993 assigned positive charge : 515.5504 centred at (gu) : 88.42348 91.00417 89.44078 assigned negative charge : -519.5518 centred at (gu) : 88.40976 91.02232 89.44514 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7554 nv = 96 ne = 84 npr = 69434 no. pairs analyzed = 69434 no. exposed pairs = 4094 no. arc points = 28500 no. surface atoms = 1391 nbur = 2028 mkacc time = 0.1800000 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 = 1.484000 m= 329 mr = 4205 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2972 ## 340 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9623 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1437867E-10 -7.2029921E-10 midg,1,midg; midg,igrid,midg -2.6642738E-10 -1.4159536E-09 1,midg,midg; igrid,midg,midg -1.4790945E-09 -3.0203098E-10 gauss-seidel spectral radius is 0.9844284 estimated iterations to convergence 66 setup time was (sec) 0.7000000 now iterating at: 14:10:43 rms-change max change #iterations 0.1038546 14.49482 at 10iterations 7.8451531E-03 1.045181 at 20iterations 6.4556091E-04 9.3013763E-02 at 30iterations 7.8718236E-05 1.2716293E-02 at 40iterations 1.7881252E-05 3.6087036E-03 at 50iterations finished qdiffx linear iterations at : 14:10:47 total time elapsed so far: 4.580000 # loops : 50 mean,max change (kT/e) : 1.7881252E-05 3.6087036E-03 energy calculations done at 4.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.740000 DelPhi exited at 14:10:47 4.748u 0.408s 0:05.59 91.9% 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 14:10:47 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3419 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: 1.725280 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): -10.03000 43.15900 ymin,ymax (A): 6.634000 62.70900 zmin,zma (A): -3.710000 58.19300 x,y,z range (A): 53.18900 56.07500 61.90300 scale (grids/A): 1.725280 object centre (A): 16.56450 34.67150 27.24150 number of atom coordinates read : 3419 total number of charged atoms : 3275 net assigned charge : -3.999993 assigned positive charge : 515.5504 centred at (gu) : 85.26930 93.01150 88.32132 assigned negative charge : -519.5518 centred at (gu) : 85.22865 93.06654 88.33513 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 83050 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28500 grid for indexing accessible points = 1.400000 m= 28476 mr = 58999 m= 3449 mr = 20644 m= 112 mr = 1850 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 135 time to turn everything in is 0.7100000 number of dielectric boundary points 33583 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 286 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 25372 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) : 0.5750933 object centre at (A) : 16.56450 34.67150 27.24150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3487157E-02 -4.9501997E-03 midg,1,midg; midg,igrid,midg -4.8443419E-03 -1.1626948E-02 1,midg,midg; igrid,midg,midg 9.8383322E-04 -5.0459374E-03 gauss-seidel spectral radius is 0.9984144 estimated iterations to convergence 199 setup time was (sec) 1.150000 now iterating at: 14:10:49 rms-change max change #iterations 4.078575 189.8638 at 10iterations 1.799252 58.64907 at 20iterations 0.7962514 25.80161 at 30iterations 0.3515629 11.20833 at 40iterations 0.1549029 4.869451 at 50iterations 6.8376690E-02 2.134395 at 60iterations 3.0203259E-02 0.9756279 at 70iterations 1.3424487E-02 0.4370632 at 80iterations 5.9332149E-03 0.1727486 at 90iterations 2.6325823E-03 7.8536987E-02 at 100iterations 1.1689825E-03 3.4015656E-02 at 110iterations 5.2141940E-04 1.7621994E-02 at 120iterations finished qdiffx linear iterations at : 14:11:01 total time elapsed so far: 12.84000 # loops : 120 mean,max change (kT/e) : 5.2141940E-04 1.7621994E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 14:11:01 13.009u 0.498s 0:13.83 97.5% 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 14:11:01 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3419 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: 2.587920 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): -10.03000 43.15900 ymin,ymax (A): 6.634000 62.70900 zmin,zma (A): -3.710000 58.19300 x,y,z range (A): 53.18900 56.07500 61.90300 scale (grids/A): 2.587920 object centre (A): 16.56450 34.67150 27.24150 number of atom coordinates read : 3419 total number of charged atoms : 3275 net assigned charge : -3.999993 assigned positive charge : 515.5504 centred at (gu) : 82.90395 94.51686 87.48186 assigned negative charge : -519.5518 centred at (gu) : 82.84289 94.59976 87.50259 start vw surface at 0.1300000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 192958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28500 grid for indexing accessible points = 1.400000 m= 96316 mr = 143535 m= 30230 mr = 78581 m= 5678 mr = 23622 m= 537 mr = 3897 m= 13 mr = 291 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 388 time to turn everything in is 1.700000 number of dielectric boundary points 75807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 26192 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) : 1.725280 object centre at (A) : 16.56450 34.67150 27.24150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1943521 -7.4767619E-02 midg,1,midg; midg,igrid,midg -4.2699102E-02 -0.1217638 1,midg,midg; igrid,midg,midg 6.6329830E-04 -1.7013393E-02 gauss-seidel spectral radius is 0.9992115 estimated iterations to convergence 281 setup time was (sec) 2.050000 now iterating at: 14:11:04 rms-change max change #iterations 10.12617 262.1359 at 10iterations 5.837840 133.0609 at 20iterations 3.324350 64.29326 at 30iterations 1.898460 35.70798 at 40iterations 1.079667 20.12706 at 50iterations 0.6139041 11.70185 at 60iterations 0.3481427 6.551796 at 70iterations 0.1973349 3.452087 at 80iterations 0.1116491 1.957094 at 90iterations 6.2951490E-02 1.278782 at 100iterations 3.5587296E-02 0.6391048 at 110iterations 2.0112349E-02 0.3580012 at 120iterations 1.1378436E-02 0.1948590 at 130iterations 6.4240783E-03 0.1111298 at 140iterations 3.6335087E-03 6.3148499E-02 at 150iterations 2.0557523E-03 3.9794922E-02 at 160iterations 1.1669631E-03 2.0821571E-02 at 170iterations 6.6219282E-04 1.1819839E-02 at 180iterations finished qdiffx linear iterations at : 14:11:22 total time elapsed so far: 20.41000 # loops : 180 mean,max change (kT/e) : 6.6219282E-04 1.1819839E-02 energy calculations done at 20.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.58000 DelPhi exited at 14:11:23 20.586u 0.491s 0:21.59 97.5% 0+0k 0+0io 0pf+0w