Sun Oct 9 12:29:25 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 12:29:25 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 = 2394 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: 0.6761761 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): -5.530000 44.48800 ymin,ymax (A): -13.98100 38.66800 zmin,zma (A): 2.472000 45.41100 x,y,z range (A): 50.01800 52.64900 42.93900 scale (grids/A): 0.6761761 object centre (A): 19.47900 12.34350 23.94150 number of atom coordinates read : 2394 total number of charged atoms : 2251 net assigned charge : 1.500025 assigned positive charge : 364.3139 centred at (gu) : 89.31342 90.62477 90.49659 assigned negative charge : -362.8145 centred at (gu) : 89.32367 90.86389 90.54311 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7328 nv = 96 ne = 84 npr = 47940 no. pairs analyzed = 47940 no. exposed pairs = 3011 no. arc points = 20891 no. surface atoms = 1012 nbur = 1382 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 4080 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.2700000 number of dielectric boundary points 3604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1934 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8525 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7412640E-08 -7.2426452E-09 midg,1,midg; midg,igrid,midg 6.2468757E-08 -7.0063592E-08 1,midg,midg; igrid,midg,midg 1.0657751E-08 3.1705560E-09 gauss-seidel spectral radius is 0.9886402 estimated iterations to convergence 77 setup time was (sec) 0.5000000 now iterating at: 12:29:26 rms-change max change #iterations 0.1751042 25.62418 at 10iterations 1.9991472E-02 2.386838 at 20iterations 2.6328096E-03 0.3382492 at 30iterations 5.0654280E-04 8.0757141E-02 at 40iterations 1.4444666E-04 2.0011902E-02 at 50iterations finished qdiffx linear iterations at : 12:29:28 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.4444666E-04 2.0011902E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 12:29:29 3.345u 0.220s 0:03.85 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 12:29:29 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 = 2394 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: 2.028528 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): -5.530000 44.48800 ymin,ymax (A): -13.98100 38.66800 zmin,zma (A): 2.472000 45.41100 x,y,z range (A): 50.01800 52.64900 42.93900 scale (grids/A): 2.028528 object centre (A): 19.47900 12.34350 23.94150 number of atom coordinates read : 2394 total number of charged atoms : 2251 net assigned charge : 1.500025 assigned positive charge : 364.3139 centred at (gu) : 87.93987 91.87359 91.48927 assigned negative charge : -362.8145 centred at (gu) : 87.97086 92.59135 91.62917 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 78617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20891 grid for indexing accessible points = 1.400000 m= 29652 mr = 54807 m= 5061 mr = 22085 m= 357 mr = 3282 m= 5 mr = 152 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3348 time to turn everything in is 0.5800000 number of dielectric boundary points 33366 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 17812 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) : 0.6761761 object centre at (A) : 19.47900 12.34350 23.94150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5511997E-02 5.3078383E-03 midg,1,midg; midg,igrid,midg 1.9277671E-02 -9.1797836E-02 1,midg,midg; igrid,midg,midg 4.8845429E-02 -6.8548573E-03 gauss-seidel spectral radius is 0.9987707 estimated iterations to convergence 226 setup time was (sec) 0.8700000 now iterating at: 12:29:30 rms-change max change #iterations 4.627342 194.2730 at 10iterations 2.239180 76.17000 at 20iterations 1.086226 33.79773 at 30iterations 0.5288185 18.33936 at 40iterations 0.2573041 7.785957 at 50iterations 0.1254430 3.842754 at 60iterations 6.1174363E-02 1.761005 at 70iterations 2.9858703E-02 0.9061890 at 80iterations 1.4710810E-02 0.4663391 at 90iterations 7.2866641E-03 0.2426453 at 100iterations 3.6602546E-03 0.1301746 at 110iterations 1.8930098E-03 5.8582306E-02 at 120iterations finished qdiffx linear iterations at : 12:29:37 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 1.8930098E-03 5.8582306E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 12:29:37 7.631u 0.219s 0:08.12 96.5% 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 Sun Oct 9 2011 at 12:29:37 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 = 2394 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: 3.042793 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): -5.530000 44.48800 ymin,ymax (A): -13.98100 38.66800 zmin,zma (A): 2.472000 45.41100 x,y,z range (A): 50.01800 52.64900 42.93900 scale (grids/A): 3.042793 object centre (A): 19.47900 12.34350 23.94150 number of atom coordinates read : 2394 total number of charged atoms : 2251 net assigned charge : 1.500025 assigned positive charge : 364.3139 centred at (gu) : 86.90966 92.81028 92.23391 assigned negative charge : -362.8145 centred at (gu) : 86.95631 93.88696 92.44361 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 181484 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20891 grid for indexing accessible points = 1.400000 m= 94554 mr = 132603 m= 35756 mr = 77685 m= 9261 mr = 29089 m= 1626 mr = 7060 m= 149 mr = 1141 m= 1 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 10865 time to turn everything in is 1.430000 number of dielectric boundary points 75167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 18008 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) : 2.028528 object centre at (A) : 19.47900 12.34350 23.94150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3750656 -1.6003534E-02 midg,1,midg; midg,igrid,midg 0.4595667 -1.019184 1,midg,midg; igrid,midg,midg 0.5412397 -0.2473457 gauss-seidel spectral radius is 0.9992841 estimated iterations to convergence 295 setup time was (sec) 1.750000 now iterating at: 12:29:39 rms-change max change #iterations 10.56477 494.9047 at 10iterations 6.222642 132.4946 at 20iterations 3.672385 84.32455 at 30iterations 2.152822 41.19573 at 40iterations 1.260674 24.31665 at 50iterations 0.7367335 13.87161 at 60iterations 0.4316602 8.201485 at 70iterations 0.2515664 4.734886 at 80iterations 0.1464512 2.704475 at 90iterations 8.5508004E-02 1.558498 at 100iterations 4.9983729E-02 0.8654015 at 110iterations 2.9223761E-02 0.5027103 at 120iterations 1.7166069E-02 0.3172112 at 130iterations 1.0218548E-02 0.1917648 at 140iterations 6.1782980E-03 0.1169968 at 150iterations 3.8596680E-03 7.7293396E-02 at 160iterations 2.5235333E-03 5.3913116E-02 at 170iterations 1.7509292E-03 3.6999702E-02 at 180iterations finished qdiffx linear iterations at : 12:29:50 total time elapsed so far: 12.42000 # loops : 180 mean,max change (kT/e) : 1.7509292E-03 3.6999702E-02 energy calculations done at 12.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 12:29:50 12.597u 0.242s 0:13.11 97.8% 0+0k 0+0io 0pf+0w