Mon Oct 10 17:01:44 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 17:01:44 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3013 !!! WARNING: HIT 107 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6134970 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): 13.62100 71.14000 ymin,ymax (A): 3.916000 51.00600 zmin,zma (A): 7.791000 65.81900 x,y,z range (A): 57.51900 47.09000 58.02800 scale (grids/A): 0.6134970 object centre (A): 42.38050 27.46100 36.80500 number of atom coordinates read : 3013 total number of charged atoms : 2868 net assigned charge : -2.485966 assigned positive charge : 458.0819 centred at (gu) : 89.28932 90.39020 90.36691 assigned negative charge : -460.5691 centred at (gu) : 89.15475 90.47344 90.48277 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7621 nv = 96 ne = 84 npr = 59922 no. pairs analyzed = 59922 no. exposed pairs = 3909 no. arc points = 27719 no. surface atoms = 1325 nbur = 1688 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 346 mr = 3980 m= 0 mr = 31 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2766 ## 279 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9406 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4700879E-09 -9.9339257E-09 midg,1,midg; midg,igrid,midg 3.5396532E-09 -7.6117113E-09 1,midg,midg; igrid,midg,midg -1.2213193E-08 6.0674310E-09 gauss-seidel spectral radius is 0.9862863 estimated iterations to convergence 70 setup time was (sec) 0.5400000 now iterating at: 17:01:45 rms-change max change #iterations 0.1306595 19.14433 at 10iterations 1.1762470E-02 1.599092 at 20iterations 1.0323739E-03 0.1448822 at 30iterations 9.6141506E-05 1.5613556E-02 at 40iterations 8.6702466E-06 1.4190674E-03 at 50iterations finished qdiffx linear iterations at : 17:01:47 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 8.6702466E-06 1.4190674E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 17:01:49 3.138u 0.157s 0:04.42 74.2% 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 Mon Oct 10 2011 at 17:01:49 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3013 !!! WARNING: HIT 107 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.840491 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): 13.62100 71.14000 ymin,ymax (A): 3.916000 51.00600 zmin,zma (A): 7.791000 65.81900 x,y,z range (A): 57.51900 47.09000 58.02800 scale (grids/A): 1.840491 object centre (A): 42.38050 27.46100 36.80500 number of atom coordinates read : 3013 total number of charged atoms : 2868 net assigned charge : -2.485966 assigned positive charge : 458.0819 centred at (gu) : 87.86742 91.16962 91.09984 assigned negative charge : -460.5691 centred at (gu) : 87.46390 91.41997 91.44790 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82856 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27719 grid for indexing accessible points = 1.400000 m= 27304 mr = 56210 m= 3712 mr = 19224 m= 173 mr = 2044 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 938 time to turn everything in is 0.5700000 number of dielectric boundary points 36537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 213 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 22479 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) : 0.6134970 object centre at (A) : 42.38050 27.46100 36.80500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1980715E-02 -4.6642189E-04 midg,1,midg; midg,igrid,midg 3.8387685E-04 -1.7868305E-02 1,midg,midg; igrid,midg,midg -3.5528027E-02 2.8430277E-02 gauss-seidel spectral radius is 0.9985917 estimated iterations to convergence 211 setup time was (sec) 0.8300000 now iterating at: 17:01:50 rms-change max change #iterations 4.377129 190.0976 at 10iterations 2.016864 64.92960 at 20iterations 0.9280114 29.48979 at 30iterations 0.4297383 14.43319 at 40iterations 0.1986456 5.605371 at 50iterations 9.1761641E-02 2.813679 at 60iterations 4.2417519E-02 1.393478 at 70iterations 1.9646794E-02 0.6306610 at 80iterations 9.0735415E-03 0.2742205 at 90iterations 4.2053652E-03 0.1240387 at 100iterations 1.9426475E-03 5.8312893E-02 at 110iterations 8.9845987E-04 2.6957989E-02 at 120iterations finished qdiffx linear iterations at : 17:01:56 total time elapsed so far: 7.020000 # loops : 120 mean,max change (kT/e) : 8.9845987E-04 2.6957989E-02 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.220000 DelPhi exited at 17:01:58 7.225u 0.176s 0:08.85 83.5% 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 17:01:58 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3013 !!! WARNING: HIT 107 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.760736 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): 13.62100 71.14000 ymin,ymax (A): 3.916000 51.00600 zmin,zma (A): 7.791000 65.81900 x,y,z range (A): 57.51900 47.09000 58.02800 scale (grids/A): 2.760736 object centre (A): 42.38050 27.46100 36.80500 number of atom coordinates read : 3013 total number of charged atoms : 2868 net assigned charge : -2.485966 assigned positive charge : 458.0819 centred at (gu) : 86.80107 91.75426 91.64953 assigned negative charge : -460.5691 centred at (gu) : 86.19576 92.12980 92.17168 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 192114 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27719 grid for indexing accessible points = 1.400000 m= 91205 mr = 137074 m= 29970 mr = 72854 m= 6197 mr = 23027 m= 678 mr = 4254 m= 26 mr = 414 m= 0 mr = 10 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 3022 time to turn everything in is 1.390000 number of dielectric boundary points 82557 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 22942 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) : 1.840491 object centre at (A) : 42.38050 27.46100 36.80500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2378922 0.2107577 midg,1,midg; midg,igrid,midg -1.3984793E-02 -0.1426071 1,midg,midg; igrid,midg,midg -0.4183152 0.4102932 gauss-seidel spectral radius is 0.9992661 estimated iterations to convergence 291 setup time was (sec) 1.670000 now iterating at: 17:01:59 rms-change max change #iterations 10.51152 330.3839 at 10iterations 6.200602 147.0890 at 20iterations 3.628947 77.11656 at 30iterations 2.107916 47.26848 at 40iterations 1.225242 22.92880 at 50iterations 0.7097708 13.89372 at 60iterations 0.4106717 9.259190 at 70iterations 0.2368881 4.681039 at 80iterations 0.1369606 2.609364 at 90iterations 7.8998558E-02 1.413261 at 100iterations 4.5596652E-02 0.7571678 at 110iterations 2.6314927E-02 0.4762192 at 120iterations 1.5135592E-02 0.2794342 at 130iterations 8.7225009E-03 0.1555080 at 140iterations 5.0249621E-03 8.5317373E-02 at 150iterations 2.8978200E-03 5.4729462E-02 at 160iterations 1.6681305E-03 2.9627800E-02 at 170iterations 9.6146256E-04 1.8388748E-02 at 180iterations finished qdiffx linear iterations at : 17:02:09 total time elapsed so far: 11.15000 # loops : 180 mean,max change (kT/e) : 9.6146256E-04 1.8388748E-02 energy calculations done at 11.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.32000 DelPhi exited at 17:02:10 11.324u 0.174s 0:12.18 94.3% 0+0k 0+0io 0pf+0w