Sun Oct 9 15:20:51 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 Sun Oct 9 2011 at 15:20:52 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5581 !!! WARNING: HIR 542 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: 0.5258183 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): 19.96500 87.66900 ymin,ymax (A): 44.28900 107.5180 zmin,zma (A): 33.46700 93.99900 x,y,z range (A): 67.70399 63.22900 60.53200 scale (grids/A): 0.5258183 object centre (A): 53.81700 75.90350 63.73300 number of atom coordinates read : 5581 total number of charged atoms : 5409 net assigned charge : -4.485951 assigned positive charge : 852.5334 centred at (gu) : 89.77069 89.59661 88.73885 assigned negative charge : -857.0269 centred at (gu) : 89.73902 89.72869 88.68685 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 9439 nv = 96 ne = 84 npr = 115589 no. pairs analyzed = 115589 no. exposed pairs = 6530 no. arc points = 44580 no. surface atoms = 2186 nbur = 3395 mkacc time = 0.2000000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 390 mr = 5170 m= 0 mr = 20 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.3800000 number of dielectric boundary points 4639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4278 ## 552 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 12746 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9250749E-10 1.2913959E-10 midg,1,midg; midg,igrid,midg 7.0933320E-10 -8.1699975E-10 1,midg,midg; igrid,midg,midg -3.2569933E-10 5.9221940E-11 gauss-seidel spectral radius is 0.9815447 estimated iterations to convergence 61 setup time was (sec) 0.5800000 now iterating at: 15:20:52 rms-change max change #iterations 8.7221041E-02 14.19871 at 10iterations 7.1413345E-03 1.084059 at 20iterations 1.8238069E-03 0.3138809 at 30iterations 6.7969953E-04 0.1215343 at 40iterations 2.5726089E-04 4.6535492E-02 at 50iterations finished qdiffx linear iterations at : 15:20:55 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 2.5726089E-04 4.6535492E-02 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 15:20:56 3.613u 0.160s 0:04.05 93.0% 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 Sun Oct 9 2011 at 15:20:56 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5581 !!! WARNING: HIR 542 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: 1.577455 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): 19.96500 87.66900 ymin,ymax (A): 44.28900 107.5180 zmin,zma (A): 33.46700 93.99900 x,y,z range (A): 67.70399 63.22900 60.53200 scale (grids/A): 1.577455 object centre (A): 53.81700 75.90350 63.73300 number of atom coordinates read : 5581 total number of charged atoms : 5409 net assigned charge : -4.485951 assigned positive charge : 852.5334 centred at (gu) : 89.31062 88.78823 86.21520 assigned negative charge : -857.0269 centred at (gu) : 89.21694 89.18600 86.06060 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 106783 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44580 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 33168 mr = 75242 m= 3494 mr = 23294 m= 81 mr = 1732 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1593 time to turn everything in is 0.5300000 number of dielectric boundary points 43258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 464 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 40982 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) : 0.5258183 object centre at (A) : 53.81700 75.90350 63.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3230943E-02 -1.9386312E-03 midg,1,midg; midg,igrid,midg 1.1695666E-02 -3.0858934E-02 1,midg,midg; igrid,midg,midg -1.7286053E-02 1.8594096E-03 gauss-seidel spectral radius is 0.9982885 estimated iterations to convergence 192 setup time was (sec) 0.7400000 now iterating at: 15:20:57 rms-change max change #iterations 4.496499 165.7249 at 10iterations 1.926236 72.81334 at 20iterations 0.8252571 25.76056 at 30iterations 0.3543683 10.83063 at 40iterations 0.1523125 4.177451 at 50iterations 6.5561101E-02 1.859326 at 60iterations 2.8408036E-02 0.8842087 at 70iterations 1.2446963E-02 0.3747101 at 80iterations 5.6107650E-03 0.1667671 at 90iterations 2.6948261E-03 8.8855743E-02 at 100iterations 1.4183054E-03 4.8023224E-02 at 110iterations 8.2614389E-04 2.7786255E-02 at 120iterations finished qdiffx linear iterations at : 15:21:04 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 8.2614389E-04 2.7786255E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.110000 DelPhi exited at 15:21:04 8.108u 0.201s 0:08.58 96.7% 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 15:21:04 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5581 !!! WARNING: HIR 542 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: 2.366182 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): 19.96500 87.66900 ymin,ymax (A): 44.28900 107.5180 zmin,zma (A): 33.46700 93.99900 x,y,z range (A): 67.70399 63.22900 60.53200 scale (grids/A): 2.366182 object centre (A): 53.81700 75.90350 63.73300 number of atom coordinates read : 5581 total number of charged atoms : 5409 net assigned charge : -4.485951 assigned positive charge : 852.5334 centred at (gu) : 88.96525 88.18165 84.32240 assigned negative charge : -857.0269 centred at (gu) : 88.82531 88.77905 84.09078 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 248970 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44580 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 115205 mr = 184688 m= 33170 mr = 91695 m= 5302 mr = 25266 m= 313 mr = 3484 m= 3 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 5557 time to turn everything in is 1.280000 number of dielectric boundary points 97712 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 43188 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) : 1.577455 object centre at (A) : 53.81700 75.90350 63.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1766644 -7.4762627E-02 midg,1,midg; midg,igrid,midg 0.2738319 -0.4454019 1,midg,midg; igrid,midg,midg -0.3185694 9.3285732E-02 gauss-seidel spectral radius is 0.9992226 estimated iterations to convergence 283 setup time was (sec) 1.530000 now iterating at: 15:21:06 rms-change max change #iterations 11.95388 301.9013 at 10iterations 6.989080 144.6337 at 20iterations 4.061917 78.99072 at 30iterations 2.356614 46.45543 at 40iterations 1.355998 26.43969 at 50iterations 0.7770396 14.49747 at 60iterations 0.4458210 8.169910 at 70iterations 0.2546000 4.517443 at 80iterations 0.1453034 2.473202 at 90iterations 8.2875401E-02 1.345825 at 100iterations 4.7284111E-02 0.8065147 at 110iterations 2.6961213E-02 0.4791050 at 120iterations 1.5343488E-02 0.2427750 at 130iterations 8.7559316E-03 0.1596222 at 140iterations 5.0214143E-03 8.3900452E-02 at 150iterations 2.8973126E-03 4.7583580E-02 at 160iterations 1.6860003E-03 2.9468536E-02 at 170iterations 1.0024708E-03 1.8840790E-02 at 180iterations finished qdiffx linear iterations at : 15:21:18 total time elapsed so far: 13.37000 # loops : 180 mean,max change (kT/e) : 1.0024708E-03 1.8840790E-02 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.51000 DelPhi exited at 15:21:18 13.510u 0.224s 0:14.01 98.0% 0+0k 0+0io 0pf+0w