Sat Oct 8 15:54:05 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 Sat Oct 8 2011 at 15:54:05 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 = 2255 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6491020 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): -2.388000 45.54000 ymin,ymax (A): -14.86300 29.80200 zmin,zma (A): -19.21200 35.63300 x,y,z range (A): 47.92800 44.66500 54.84500 scale (grids/A): 0.6491020 object centre (A): 21.57600 7.469500 8.210502 number of atom coordinates read : 2255 total number of charged atoms : 2194 net assigned charge : 3.000000 assigned positive charge : 335.6093 centred at (gu) : 90.55861 88.31644 90.24773 assigned negative charge : -332.6099 centred at (gu) : 90.61260 88.45074 90.32490 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6503 nv = 96 ne = 84 npr = 44833 no. pairs analyzed = 44833 no. exposed pairs = 2893 no. arc points = 20058 no. surface atoms = 992 nbur = 1263 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 3545 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3000000 number of dielectric boundary points 3284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1972 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7750 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4372296E-08 -4.7723838E-09 midg,1,midg; midg,igrid,midg 3.1939649E-08 -8.2602956E-09 1,midg,midg; igrid,midg,midg 1.0882975E-08 -1.7516133E-09 gauss-seidel spectral radius is 0.9876739 estimated iterations to convergence 74 setup time was (sec) 0.6000000 now iterating at: 15:54:06 rms-change max change #iterations 0.1377218 20.37899 at 10iterations 1.4000878E-02 2.009363 at 20iterations 1.5632987E-03 0.2426376 at 30iterations 2.3409972E-04 3.2552242E-02 at 40iterations 5.6895711E-05 7.8233480E-03 at 50iterations finished qdiffx linear iterations at : 15:54:11 total time elapsed so far: 4.990000 # loops : 50 mean,max change (kT/e) : 5.6895711E-05 7.8233480E-03 energy calculations done at 4.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.170000 DelPhi exited at 15:54:11 5.174u 0.448s 0:05.89 95.2% 0+0k 0+0io 6pf+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 Sat Oct 8 2011 at 15:54:11 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 = 2255 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.947306 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): -2.388000 45.54000 ymin,ymax (A): -14.86300 29.80200 zmin,zma (A): -19.21200 35.63300 x,y,z range (A): 47.92800 44.66500 54.84500 scale (grids/A): 1.947306 object centre (A): 21.57600 7.469500 8.210502 number of atom coordinates read : 2255 total number of charged atoms : 2194 net assigned charge : 3.000000 assigned positive charge : 335.6093 centred at (gu) : 91.67528 84.94891 90.74259 assigned negative charge : -332.6099 centred at (gu) : 91.83758 85.35207 90.97459 start vw surface at 0.1000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 70246 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20058 grid for indexing accessible points = 1.400000 m= 25723 mr = 48691 m= 4491 mr = 18869 m= 271 mr = 2879 m= 3 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 802 time to turn everything in is 0.5900000 number of dielectric boundary points 30199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17310 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) : 0.6491020 object centre at (A) : 21.57600 7.469500 8.210502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8880827E-02 -1.0222895E-02 midg,1,midg; midg,igrid,midg 2.3616262E-02 -5.7113338E-03 1,midg,midg; igrid,midg,midg 3.4083929E-03 -4.0037327E-02 gauss-seidel spectral radius is 0.9986614 estimated iterations to convergence 217 setup time was (sec) 0.9700000 now iterating at: 15:54:13 rms-change max change #iterations 4.056772 159.5632 at 10iterations 1.911651 71.34894 at 20iterations 0.9031676 27.68798 at 30iterations 0.4278621 14.70630 at 40iterations 0.2015065 6.327861 at 50iterations 9.5209412E-02 3.177424 at 60iterations 4.4940360E-02 1.380595 at 70iterations 2.1251647E-02 0.8113871 at 80iterations 1.0078072E-02 0.3089950 at 90iterations 4.7675935E-03 0.1611328 at 100iterations 2.2734720E-03 6.9406509E-02 at 110iterations 1.0832908E-03 3.3936501E-02 at 120iterations finished qdiffx linear iterations at : 15:54:24 total time elapsed so far: 12.36000 # loops : 120 mean,max change (kT/e) : 1.0832908E-03 3.3936501E-02 energy calculations done at 12.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 15:54:25 12.541u 0.525s 0:13.32 98.0% 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 Sat Oct 8 2011 at 15:54:25 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 = 2255 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.920959 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): -2.388000 45.54000 ymin,ymax (A): -14.86300 29.80200 zmin,zma (A): -19.21200 35.63300 x,y,z range (A): 47.92800 44.66500 54.84500 scale (grids/A): 2.920959 object centre (A): 21.57600 7.469500 8.210502 number of atom coordinates read : 2255 total number of charged atoms : 2194 net assigned charge : 3.000000 assigned positive charge : 335.6093 centred at (gu) : 92.51292 82.42328 91.11377 assigned negative charge : -332.6099 centred at (gu) : 92.75642 83.02819 91.46196 start vw surface at 0.1200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 162571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20058 grid for indexing accessible points = 1.400000 m= 82214 mr = 118148 m= 31120 mr = 67025 m= 8161 mr = 24918 m= 1235 mr = 6265 m= 66 mr = 833 m= 0 mr = 19 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 2509 time to turn everything in is 1.570000 number of dielectric boundary points 68159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 17552 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) : 1.947306 object centre at (A) : 21.57600 7.469500 8.210502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3032107 -5.3400207E-02 midg,1,midg; midg,igrid,midg 0.1459286 -8.9614250E-02 1,midg,midg; igrid,midg,midg 3.7711680E-02 -0.5080497 gauss-seidel spectral radius is 0.9992658 estimated iterations to convergence 291 setup time was (sec) 1.960000 now iterating at: 15:54:27 rms-change max change #iterations 9.600450 518.3395 at 10iterations 5.670828 131.2356 at 20iterations 3.334359 88.34698 at 30iterations 1.950927 42.89214 at 40iterations 1.139877 25.19537 at 50iterations 0.6631629 13.56034 at 60iterations 0.3856756 7.872414 at 70iterations 0.2236758 4.238291 at 80iterations 0.1296528 2.437011 at 90iterations 7.5046681E-02 1.382984 at 100iterations 4.3432549E-02 0.7994032 at 110iterations 2.5037391E-02 0.4757671 at 120iterations 1.4489592E-02 0.2617621 at 130iterations 8.3550103E-03 0.1618595 at 140iterations 4.8273299E-03 8.7317944E-02 at 150iterations 2.7842943E-03 5.2556992E-02 at 160iterations 1.6130300E-03 3.4287453E-02 at 170iterations 9.3293778E-04 1.6404152E-02 at 180iterations finished qdiffx linear iterations at : 15:54:46 total time elapsed so far: 21.11000 # loops : 180 mean,max change (kT/e) : 9.3293778E-04 1.6404152E-02 energy calculations done at 21.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.27000 DelPhi exited at 15:54:47 21.272u 0.548s 0:22.12 98.5% 0+0k 0+0io 0pf+0w