Tue Oct 11 03:19:25 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+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 03:19:25 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2695 !!! WARNING: HIR 128 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6212589 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): -26.71300 23.93900 ymin,ymax (A): 8.445000 64.33600 zmin,zma (A): -31.30500 25.99800 x,y,z range (A): 50.65200 55.89100 57.30300 scale (grids/A): 0.6212589 object centre (A): -1.387000 36.39050 -2.653500 number of atom coordinates read : 2695 total number of charged atoms : 2547 net assigned charge : -1.985985 assigned positive charge : 397.8987 centred at (gu) : 88.61187 88.01427 92.24389 assigned negative charge : -399.8857 centred at (gu) : 88.55783 87.94582 92.17230 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7218 nv = 96 ne = 84 npr = 52548 no. pairs analyzed = 52548 no. exposed pairs = 3750 no. arc points = 26656 no. surface atoms = 1239 nbur = 1456 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 355 mr = 3607 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2596 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8574 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0794572E-09 5.7032774E-09 midg,1,midg; midg,igrid,midg -1.0035176E-08 2.0157511E-09 1,midg,midg; igrid,midg,midg -7.3658932E-09 1.5740466E-09 gauss-seidel spectral radius is 0.9866034 estimated iterations to convergence 71 setup time was (sec) 0.4200000 now iterating at: 03:19:26 rms-change max change #iterations 0.1327913 23.00154 at 10iterations 1.2238214E-02 2.176117 at 20iterations 1.1066220E-03 0.1456223 at 30iterations 1.0464657E-04 1.7461777E-02 at 40iterations 1.0318355E-05 1.3065338E-03 at 50iterations finished qdiffx linear iterations at : 03:19:29 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.0318355E-05 1.3065338E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 03:19:29 3.442u 0.154s 0:03.88 92.5% 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 Tue Oct 11 2011 at 03:19:29 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2695 !!! WARNING: HIR 128 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.863777 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): -26.71300 23.93900 ymin,ymax (A): 8.445000 64.33600 zmin,zma (A): -31.30500 25.99800 x,y,z range (A): 50.65200 55.89100 57.30300 scale (grids/A): 1.863777 object centre (A): -1.387000 36.39050 -2.653500 number of atom coordinates read : 2695 total number of charged atoms : 2547 net assigned charge : -1.985985 assigned positive charge : 397.8987 centred at (gu) : 85.83489 84.04213 96.73101 assigned negative charge : -399.8857 centred at (gu) : 85.67332 83.83727 96.51669 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77013 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26656 grid for indexing accessible points = 1.400000 m= 26717 mr = 50717 m= 3997 mr = 18692 m= 189 mr = 2254 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 36216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 19985 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) : 0.6212589 object centre at (A) : -1.387000 36.39050 -2.653500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9359044E-02 2.9826481E-02 midg,1,midg; midg,igrid,midg -4.1019686E-02 -6.9298297E-03 1,midg,midg; igrid,midg,midg -1.9165559E-03 7.4720476E-03 gauss-seidel spectral radius is 0.9985999 estimated iterations to convergence 212 setup time was (sec) 0.6000000 now iterating at: 03:19:30 rms-change max change #iterations 4.189411 185.7510 at 10iterations 1.937777 66.89598 at 20iterations 0.8995551 29.38883 at 30iterations 0.4159734 13.46576 at 40iterations 0.1925719 6.577435 at 50iterations 8.9254551E-02 2.900996 at 60iterations 4.1481867E-02 1.362671 at 70iterations 1.9187370E-02 0.6180615 at 80iterations 8.8990852E-03 0.2800579 at 90iterations 4.1148560E-03 0.1257343 at 100iterations 1.9050002E-03 6.4632416E-02 at 110iterations 8.8423409E-04 2.6563644E-02 at 120iterations finished qdiffx linear iterations at : 03:19:37 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 8.8423409E-04 2.6563644E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 03:19:37 7.899u 0.206s 0:08.40 96.3% 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 03:19:37 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2695 !!! WARNING: HIR 128 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.795665 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): -26.71300 23.93900 ymin,ymax (A): 8.445000 64.33600 zmin,zma (A): -31.30500 25.99800 x,y,z range (A): 50.65200 55.89100 57.30300 scale (grids/A): 2.795665 object centre (A): -1.387000 36.39050 -2.653500 number of atom coordinates read : 2695 total number of charged atoms : 2547 net assigned charge : -1.985985 assigned positive charge : 397.8987 centred at (gu) : 83.75217 81.06316 100.0965 assigned negative charge : -399.8857 centred at (gu) : 83.50990 80.75591 99.77486 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 177687 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26656 grid for indexing accessible points = 1.400000 m= 86373 mr = 123491 m= 30465 mr = 68266 m= 6970 mr = 23610 m= 822 mr = 4873 m= 35 mr = 480 m= 0 mr = 4 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9700000 number of dielectric boundary points 81628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 20374 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) : 1.863777 object centre at (A) : -1.387000 36.39050 -2.653500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7941515 0.3828208 midg,1,midg; midg,igrid,midg -0.3070541 -9.7074427E-02 1,midg,midg; igrid,midg,midg -1.9234475E-02 4.3631449E-02 gauss-seidel spectral radius is 0.9992730 estimated iterations to convergence 293 setup time was (sec) 1.220000 now iterating at: 03:19:39 rms-change max change #iterations 10.04233 340.7333 at 10iterations 5.999883 139.5608 at 20iterations 3.541005 77.23858 at 30iterations 2.089265 46.07092 at 40iterations 1.226523 27.36692 at 50iterations 0.7165130 15.41602 at 60iterations 0.4182988 8.108331 at 70iterations 0.2429465 5.358984 at 80iterations 0.1411304 3.073701 at 90iterations 8.1700958E-02 1.511139 at 100iterations 4.7470454E-02 0.9730189 at 110iterations 2.7470322E-02 0.5490723 at 120iterations 1.5923649E-02 0.3268380 at 130iterations 9.2163142E-03 0.1830559 at 140iterations 5.3201159E-03 9.6855998E-02 at 150iterations 3.0790940E-03 5.9040070E-02 at 160iterations 1.7771889E-03 3.3058882E-02 at 170iterations 1.0303922E-03 2.0224571E-02 at 180iterations finished qdiffx linear iterations at : 03:19:50 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 1.0303922E-03 2.0224571E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 03:19:51 12.898u 0.215s 0:13.45 97.3% 0+0k 0+0io 0pf+0w