Mon Oct 10 09:45:18 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 Mon Oct 10 2011 at 09:45:18 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 = 2902 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5817754 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): -18.42000 35.29500 ymin,ymax (A): -63.56200 -4.147000 zmin,zma (A): -4.150000 57.04200 x,y,z range (A): 53.71500 59.41500 61.19200 scale (grids/A): 0.5817754 object centre (A): 8.437499 -33.85450 26.44600 number of atom coordinates read : 2902 total number of charged atoms : 2751 net assigned charge : 7.000026 assigned positive charge : 428.7128 centred at (gu) : 89.34833 89.41339 87.83427 assigned negative charge : -421.7133 centred at (gu) : 89.48625 89.33409 87.66444 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6650 nv = 96 ne = 84 npr = 56121 no. pairs analyzed = 56121 no. exposed pairs = 4293 no. arc points = 31475 no. surface atoms = 1439 nbur = 1463 mkacc time = 0.1200000 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 = 1.512000 m= 326 mr = 2920 m= 3 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3131 ## 352 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8369 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6249228E-09 3.2520635E-09 midg,1,midg; midg,igrid,midg -7.8263104E-11 2.9954974E-09 1,midg,midg; igrid,midg,midg 5.4609002E-09 -1.1712930E-09 gauss-seidel spectral radius is 0.9847630 estimated iterations to convergence 67 setup time was (sec) 0.5700000 now iterating at: 09:45:19 rms-change max change #iterations 9.7000599E-02 15.92503 at 10iterations 7.6331845E-03 1.263020 at 20iterations 6.0678838E-04 0.1017032 at 30iterations 6.3337488E-05 1.2588501E-02 at 40iterations 1.0292299E-05 1.9931793E-03 at 50iterations finished qdiffx linear iterations at : 09:45:22 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.0292299E-05 1.9931793E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 09:45:22 3.369u 0.186s 0:03.84 92.1% 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 09:45:22 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 = 2902 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.745326 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): -18.42000 35.29500 ymin,ymax (A): -63.56200 -4.147000 zmin,zma (A): -4.150000 57.04200 x,y,z range (A): 53.71500 59.41500 61.19200 scale (grids/A): 1.745326 object centre (A): 8.437499 -33.85450 26.44600 number of atom coordinates read : 2902 total number of charged atoms : 2751 net assigned charge : 7.000026 assigned positive charge : 428.7128 centred at (gu) : 88.04465 88.23960 83.50210 assigned negative charge : -421.7133 centred at (gu) : 88.45853 88.00169 82.99284 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31475 grid for indexing accessible points = 1.400000 m= 22491 mr = 43444 m= 2937 mr = 14254 m= 111 mr = 1288 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 286 time to turn everything in is 0.5400000 number of dielectric boundary points 37470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 294 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21441 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) : 0.5817754 object centre at (A) : 8.437499 -33.85450 26.44600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2178137E-03 1.3479846E-02 midg,1,midg; midg,igrid,midg 2.2037245E-02 4.1356470E-02 1,midg,midg; igrid,midg,midg 1.1621527E-02 1.0004928E-02 gauss-seidel spectral radius is 0.9984367 estimated iterations to convergence 201 setup time was (sec) 0.8300000 now iterating at: 09:45:23 rms-change max change #iterations 3.741641 169.8036 at 10iterations 1.639086 67.71029 at 20iterations 0.7271010 26.20127 at 30iterations 0.3191048 10.43885 at 40iterations 0.1413327 5.020584 at 50iterations 6.2525757E-02 2.193836 at 60iterations 2.7594056E-02 0.9839115 at 70iterations 1.2220677E-02 0.4291077 at 80iterations 5.4130428E-03 0.1775455 at 90iterations 2.4024914E-03 8.5477829E-02 at 100iterations 1.0620765E-03 3.6332130E-02 at 110iterations 4.7199312E-04 1.5148163E-02 at 120iterations finished qdiffx linear iterations at : 09:45:30 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 4.7199312E-04 1.5148163E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 09:45:31 7.579u 0.206s 0:08.26 94.0% 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 Mon Oct 10 2011 at 09:45:31 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 = 2902 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.617989 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): -18.42000 35.29500 ymin,ymax (A): -63.56200 -4.147000 zmin,zma (A): -4.150000 57.04200 x,y,z range (A): 53.71500 59.41500 61.19200 scale (grids/A): 2.617989 object centre (A): 8.437499 -33.85450 26.44600 number of atom coordinates read : 2902 total number of charged atoms : 2751 net assigned charge : 7.000026 assigned positive charge : 428.7128 centred at (gu) : 87.06684 87.35924 80.25290 assigned negative charge : -421.7133 centred at (gu) : 87.68757 87.00238 79.48916 start vw surface at 0.1800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 163824 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31475 grid for indexing accessible points = 1.400000 m= 73843 mr = 106928 m= 24001 mr = 55219 m= 4590 mr = 17053 m= 349 mr = 2677 m= 8 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 1087 time to turn everything in is 1.330000 number of dielectric boundary points 84624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 22000 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) : 1.745326 object centre at (A) : 8.437499 -33.85450 26.44600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6138397E-02 9.0513527E-02 midg,1,midg; midg,igrid,midg 0.4788532 0.5396137 1,midg,midg; igrid,midg,midg 1.8330015E-02 0.1694944 gauss-seidel spectral radius is 0.9992333 estimated iterations to convergence 285 setup time was (sec) 1.640000 now iterating at: 09:45:32 rms-change max change #iterations 9.548486 282.3998 at 10iterations 5.649285 165.3916 at 20iterations 3.300527 76.69418 at 30iterations 1.910764 42.90861 at 40iterations 1.101930 27.60830 at 50iterations 0.6330734 12.66889 at 60iterations 0.3641729 7.131563 at 70iterations 0.2082635 4.001080 at 80iterations 0.1191819 2.751088 at 90iterations 6.7970976E-02 1.468723 at 100iterations 3.8770612E-02 0.7752190 at 110iterations 2.2063065E-02 0.5132599 at 120iterations 1.2583387E-02 0.2418613 at 130iterations 7.1510570E-03 0.1433830 at 140iterations 4.0706629E-03 8.0471039E-02 at 150iterations 2.3139941E-03 4.6497345E-02 at 160iterations 1.3142762E-03 2.8198242E-02 at 170iterations 7.4757327E-04 1.4519691E-02 at 180iterations finished qdiffx linear iterations at : 09:45:43 total time elapsed so far: 12.13000 # loops : 180 mean,max change (kT/e) : 7.4757327E-04 1.4519691E-02 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 09:45:44 12.322u 0.240s 0:12.95 96.9% 0+0k 0+0io 0pf+0w