Mon Oct 10 21:10:21 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 Mon Oct 10 2011 at 21:10:21 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2712 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6225408 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): -10.21000 45.46900 ymin,ymax (A): 32.18200 85.11400 zmin,zma (A): -11.45400 45.73100 x,y,z range (A): 55.67900 52.93200 57.18501 scale (grids/A): 0.6225408 object centre (A): 17.62950 58.64800 17.13850 number of atom coordinates read : 2712 total number of charged atoms : 2575 net assigned charge : 1.500006 assigned positive charge : 401.5747 centred at (gu) : 89.39259 89.04546 89.62421 assigned negative charge : -400.0758 centred at (gu) : 89.36770 89.02517 89.62916 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7236 nv = 96 ne = 84 npr = 53273 no. pairs analyzed = 53273 no. exposed pairs = 3857 no. arc points = 27708 no. surface atoms = 1261 nbur = 1451 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 3514 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4092 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2663 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8622 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8361528E-09 8.9285124E-10 midg,1,midg; midg,igrid,midg -2.2736794E-10 2.2933107E-09 1,midg,midg; igrid,midg,midg -5.9466948E-10 2.7666447E-09 gauss-seidel spectral radius is 0.9866627 estimated iterations to convergence 71 setup time was (sec) 0.6500000 now iterating at: 21:10:22 rms-change max change #iterations 0.1288910 21.88715 at 10iterations 1.1863331E-02 1.848080 at 20iterations 1.1397426E-03 0.1960297 at 30iterations 1.1987352E-04 1.7740250E-02 at 40iterations 1.8095123E-05 2.3469925E-03 at 50iterations finished qdiffx linear iterations at : 21:10:26 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 1.8095123E-05 2.3469925E-03 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.670000 DelPhi exited at 21:10:27 4.677u 0.379s 0:05.50 91.6% 0+0k 0+0io 4pf+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 21:10:27 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2712 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.867622 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): -10.21000 45.46900 ymin,ymax (A): 32.18200 85.11400 zmin,zma (A): -11.45400 45.73100 x,y,z range (A): 55.67900 52.93200 57.18501 scale (grids/A): 1.867622 object centre (A): 17.62950 58.64800 17.13850 number of atom coordinates read : 2712 total number of charged atoms : 2575 net assigned charge : 1.500006 assigned positive charge : 401.5747 centred at (gu) : 88.17727 87.13589 88.87216 assigned negative charge : -400.0758 centred at (gu) : 88.10314 87.07552 88.88751 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27708 grid for indexing accessible points = 1.400000 m= 26819 mr = 50058 m= 4326 mr = 18311 m= 280 mr = 2266 m= 4 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 37937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 20206 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) : 0.6225408 object centre at (A) : 17.62950 58.64800 17.13850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0427639E-03 -1.6107596E-02 midg,1,midg; midg,igrid,midg 4.6589300E-02 1.9567100E-02 1,midg,midg; igrid,midg,midg -3.3262467E-03 -2.0498494E-03 gauss-seidel spectral radius is 0.9986177 estimated iterations to convergence 213 setup time was (sec) 0.9500000 now iterating at: 21:10:28 rms-change max change #iterations 4.158496 165.1504 at 10iterations 1.924780 70.38750 at 20iterations 0.8931910 30.43820 at 30iterations 0.4137075 13.03341 at 40iterations 0.1924140 6.357089 at 50iterations 8.9361839E-02 2.944424 at 60iterations 4.1645057E-02 1.358174 at 70iterations 1.9448699E-02 0.6272030 at 80iterations 9.0448214E-03 0.2771950 at 90iterations 4.2086714E-03 0.1361542 at 100iterations 1.9671540E-03 6.6297531E-02 at 110iterations 9.1915048E-04 2.7526855E-02 at 120iterations finished qdiffx linear iterations at : 21:10:38 total time elapsed so far: 10.70000 # loops : 120 mean,max change (kT/e) : 9.1915048E-04 2.7526855E-02 energy calculations done at 10.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.96000 DelPhi exited at 21:10:39 10.968u 0.461s 0:11.81 96.6% 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 21:10:39 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2712 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.801434 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): -10.21000 45.46900 ymin,ymax (A): 32.18200 85.11400 zmin,zma (A): -11.45400 45.73100 x,y,z range (A): 55.67900 52.93200 57.18501 scale (grids/A): 2.801434 object centre (A): 17.62950 58.64800 17.13850 number of atom coordinates read : 2712 total number of charged atoms : 2575 net assigned charge : 1.500006 assigned positive charge : 401.5747 centred at (gu) : 87.26576 85.70376 88.30805 assigned negative charge : -400.0758 centred at (gu) : 87.15462 85.61320 88.33109 start vw surface at 0.1200000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 178337 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27708 grid for indexing accessible points = 1.400000 m= 86333 mr = 122791 m= 30952 mr = 67068 m= 7609 mr = 23236 m= 1145 mr = 5116 m= 71 mr = 660 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.680000 number of dielectric boundary points 85554 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 20598 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) : 1.867622 object centre at (A) : 17.62950 58.64800 17.13850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2107434E-02 -0.1359997 midg,1,midg; midg,igrid,midg 0.8379636 0.3236318 1,midg,midg; igrid,midg,midg 0.1356083 -4.1441299E-02 gauss-seidel spectral radius is 0.9992731 estimated iterations to convergence 293 setup time was (sec) 2.020000 now iterating at: 21:10:41 rms-change max change #iterations 10.12278 344.6697 at 10iterations 6.057472 142.2186 at 20iterations 3.578425 86.83678 at 30iterations 2.111625 45.09592 at 40iterations 1.240224 24.82694 at 50iterations 0.7232074 13.45020 at 60iterations 0.4226933 8.568409 at 70iterations 0.2456257 5.115601 at 80iterations 0.1429892 3.019600 at 90iterations 8.2985997E-02 1.614027 at 100iterations 4.8126951E-02 0.9113655 at 110iterations 2.7876390E-02 0.5414314 at 120iterations 1.6158018E-02 0.3078308 at 130iterations 9.4033293E-03 0.1888072 at 140iterations 5.4339054E-03 9.3784332E-02 at 150iterations 3.1702882E-03 6.1369896E-02 at 160iterations 1.8504023E-03 3.3615112E-02 at 170iterations 1.0854555E-03 2.1759033E-02 at 180iterations finished qdiffx linear iterations at : 21:11:00 total time elapsed so far: 20.36000 # loops : 180 mean,max change (kT/e) : 1.0854555E-03 2.1759033E-02 energy calculations done at 20.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.54000 DelPhi exited at 21:11:00 20.542u 0.475s 0:21.30 98.6% 0+0k 0+0io 0pf+0w