Sun Oct 9 11:15:44 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 Sun Oct 9 2011 at 11:15:44 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 !!! WARNING: HIR 209 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: 0.6231075 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): -44.59200 12.54100 ymin,ymax (A): -25.10700 24.67600 zmin,zma (A): 0.1480000 57.19900 x,y,z range (A): 57.13300 49.78300 57.05100 scale (grids/A): 0.6231075 object centre (A): -16.02550 -0.2155008 28.67350 number of atom coordinates read : 2852 total number of charged atoms : 2751 net assigned charge : 1.514021 assigned positive charge : 422.9771 centred at (gu) : 89.39565 90.75323 88.81509 assigned negative charge : -421.4647 centred at (gu) : 89.38555 90.77184 88.85370 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7774 nv = 96 ne = 84 npr = 55716 no. pairs analyzed = 55716 no. exposed pairs = 3909 no. arc points = 27401 no. surface atoms = 1300 nbur = 1552 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 461 mr = 4010 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2200000 number of dielectric boundary points 4171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2714 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9342 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6469576E-09 -1.3252207E-09 midg,1,midg; midg,igrid,midg 2.3582531E-09 -1.9915500E-10 1,midg,midg; igrid,midg,midg 5.8056360E-10 1.8512296E-09 gauss-seidel spectral radius is 0.9866989 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 11:15:45 rms-change max change #iterations 0.1313785 18.67798 at 10iterations 1.2793203E-02 1.669823 at 20iterations 1.3929133E-03 0.2507439 at 30iterations 2.3139977E-04 3.8600922E-02 at 40iterations 5.5660596E-05 9.7942352E-03 at 50iterations finished qdiffx linear iterations at : 11:15:47 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 5.5660596E-05 9.7942352E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 11:15:48 3.419u 0.174s 0:03.94 90.8% 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 11:15:48 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 !!! WARNING: HIR 209 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: 1.869322 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): -44.59200 12.54100 ymin,ymax (A): -25.10700 24.67600 zmin,zma (A): 0.1480000 57.19900 x,y,z range (A): 57.13300 49.78300 57.05100 scale (grids/A): 1.869322 object centre (A): -16.02550 -0.2155008 28.67350 number of atom coordinates read : 2852 total number of charged atoms : 2751 net assigned charge : 1.514021 assigned positive charge : 422.9771 centred at (gu) : 88.18615 92.25872 86.44447 assigned negative charge : -421.4647 centred at (gu) : 88.15643 92.31550 86.56100 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83373 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27401 grid for indexing accessible points = 1.400000 m= 30493 mr = 56129 m= 5296 mr = 21542 m= 308 mr = 3186 m= 6 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 255 time to turn everything in is 0.4300000 number of dielectric boundary points 38538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 21620 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) : 0.6231075 object centre at (A) : -16.02550 -0.2155008 28.67350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4609552E-02 -1.3356900E-02 midg,1,midg; midg,igrid,midg 1.7457960E-02 1.3785291E-02 1,midg,midg; igrid,midg,midg -3.2250695E-02 1.2959858E-02 gauss-seidel spectral radius is 0.9986336 estimated iterations to convergence 214 setup time was (sec) 0.6600000 now iterating at: 11:15:49 rms-change max change #iterations 4.299479 176.1955 at 10iterations 1.997639 68.15166 at 20iterations 0.9347838 30.62968 at 30iterations 0.4367305 13.14065 at 40iterations 0.2043809 6.779611 at 50iterations 9.6044190E-02 2.951149 at 60iterations 4.4854984E-02 1.535458 at 70iterations 2.1041946E-02 0.7236500 at 80iterations 9.8907556E-03 0.3235284 at 90iterations 4.6342649E-03 0.1449280 at 100iterations 2.1812660E-03 6.8527222E-02 at 110iterations 1.0325518E-03 3.2202244E-02 at 120iterations finished qdiffx linear iterations at : 11:15:56 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 1.0325518E-03 3.2202244E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 11:15:56 7.951u 0.177s 0:08.41 96.5% 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 Sun Oct 9 2011 at 11:15:56 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 !!! WARNING: HIR 209 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: 2.803984 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): -44.59200 12.54100 ymin,ymax (A): -25.10700 24.67600 zmin,zma (A): 0.1480000 57.19900 x,y,z range (A): 57.13300 49.78300 57.05100 scale (grids/A): 2.803984 object centre (A): -16.02550 -0.2155008 28.67350 number of atom coordinates read : 2852 total number of charged atoms : 2751 net assigned charge : 1.514021 assigned positive charge : 422.9771 centred at (gu) : 87.27905 93.38791 84.66654 assigned negative charge : -421.4647 centred at (gu) : 87.23463 93.47316 84.84144 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 192412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27401 grid for indexing accessible points = 1.400000 m= 96429 mr = 136818 m= 36850 mr = 76517 m= 9701 mr = 28723 m= 1401 mr = 7020 m= 63 mr = 862 m= 0 mr = 20 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 850 time to turn everything in is 1.060000 number of dielectric boundary points 86896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 22002 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) : 1.869322 object centre at (A) : -16.02550 -0.2155008 28.67350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1608187 -0.2113078 midg,1,midg; midg,igrid,midg 0.2841648 0.1894944 1,midg,midg; igrid,midg,midg -0.4720850 0.2005019 gauss-seidel spectral radius is 0.9992747 estimated iterations to convergence 293 setup time was (sec) 1.310000 now iterating at: 11:15:58 rms-change max change #iterations 10.43001 351.5953 at 10iterations 6.227479 154.9278 at 20iterations 3.685728 100.7996 at 30iterations 2.174114 45.81517 at 40iterations 1.271693 28.10118 at 50iterations 0.7437928 13.56581 at 60iterations 0.4346616 7.974358 at 70iterations 0.2528028 4.430702 at 80iterations 0.1473696 2.747956 at 90iterations 8.5505314E-02 1.514271 at 100iterations 4.9572550E-02 0.8794556 at 110iterations 2.8751116E-02 0.5334406 at 120iterations 1.6669648E-02 0.2904863 at 130iterations 9.6903602E-03 0.1806481 at 140iterations 5.6270245E-03 9.6296310E-02 at 150iterations 3.2881568E-03 6.4395905E-02 at 160iterations 1.9282834E-03 3.4973145E-02 at 170iterations 1.1374799E-03 2.0885468E-02 at 180iterations finished qdiffx linear iterations at : 11:16:09 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 1.1374799E-03 2.0885468E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 11:16:10 13.005u 0.208s 0:13.65 96.7% 0+0k 0+0io 0pf+0w