Mon Oct 10 09:45:05 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 09:45:05 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2753 !!! WARNING: HIT 232 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5825275 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): -17.98300 35.82700 ymin,ymax (A): -64.25400 -4.488000 zmin,zma (A): -3.990000 57.12300 x,y,z range (A): 53.81000 59.76600 61.11300 scale (grids/A): 0.5825275 object centre (A): 8.922000 -34.37100 26.56650 number of atom coordinates read : 2753 total number of charged atoms : 2604 net assigned charge : 6.014014 assigned positive charge : 405.1231 centred at (gu) : 89.09104 89.38110 87.68901 assigned negative charge : -399.1094 centred at (gu) : 89.28914 89.25465 87.52319 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6254 nv = 96 ne = 84 npr = 53684 no. pairs analyzed = 53684 no. exposed pairs = 4265 no. arc points = 30428 no. surface atoms = 1400 nbur = 1353 mkacc time = 8.9999996E-02 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= 335 mr = 2653 m= 4 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2975 ## 313 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7890 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7400349E-09 2.9130307E-09 midg,1,midg; midg,igrid,midg -1.4421864E-09 3.5977914E-09 1,midg,midg; igrid,midg,midg 6.9656214E-09 -2.2620699E-09 gauss-seidel spectral radius is 0.9847890 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 09:45:05 rms-change max change #iterations 9.3539774E-02 17.22300 at 10iterations 7.1617407E-03 1.139588 at 20iterations 5.9902645E-04 9.1870308E-02 at 30iterations 6.4986627E-05 1.0896683E-02 at 40iterations 1.3542732E-05 2.4828911E-03 at 50iterations finished qdiffx linear iterations at : 09:45:08 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.3542732E-05 2.4828911E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 09:45:09 3.430u 0.192s 0:04.08 88.7% 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 Mon Oct 10 2011 at 09:45:09 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2753 !!! WARNING: HIT 232 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: 1.747582 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): -17.98300 35.82700 ymin,ymax (A): -64.25400 -4.488000 zmin,zma (A): -3.990000 57.12300 x,y,z range (A): 53.81000 59.76600 61.11300 scale (grids/A): 1.747582 object centre (A): 8.922000 -34.37100 26.56650 number of atom coordinates read : 2753 total number of charged atoms : 2604 net assigned charge : 6.014014 assigned positive charge : 405.1231 centred at (gu) : 87.27265 88.14275 83.06684 assigned negative charge : -399.1094 centred at (gu) : 87.86705 87.76383 82.56915 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66419 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30428 grid for indexing accessible points = 1.400000 m= 20892 mr = 39740 m= 2904 mr = 12898 m= 112 mr = 1381 m= 0 mr = 4 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 195 time to turn everything in is 0.3400000 number of dielectric boundary points 36304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 244 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20218 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) : 0.5825275 object centre at (A) : 8.922000 -34.37100 26.56650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5129153E-03 1.6773716E-02 midg,1,midg; midg,igrid,midg 1.5015312E-02 3.6525901E-02 1,midg,midg; igrid,midg,midg 2.0869223E-02 -2.5343278E-03 gauss-seidel spectral radius is 0.9984238 estimated iterations to convergence 200 setup time was (sec) 0.5600000 now iterating at: 09:45:10 rms-change max change #iterations 3.674851 182.6913 at 10iterations 1.613374 64.63480 at 20iterations 0.7110602 27.39326 at 30iterations 0.3124664 12.29955 at 40iterations 0.1378934 5.261826 at 50iterations 6.0743053E-02 2.105507 at 60iterations 2.6739413E-02 1.069818 at 70iterations 1.1849557E-02 0.4649630 at 80iterations 5.2225334E-03 0.1854248 at 90iterations 2.3070991E-03 8.2532167E-02 at 100iterations 1.0230753E-03 3.5079241E-02 at 110iterations 4.5381201E-04 1.5998840E-02 at 120iterations finished qdiffx linear iterations at : 09:45:17 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 4.5381201E-04 1.5998840E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 09:45:18 7.805u 0.217s 0:08.77 91.3% 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 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2753 !!! WARNING: HIT 232 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: 2.621374 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): -17.98300 35.82700 ymin,ymax (A): -64.25400 -4.488000 zmin,zma (A): -3.990000 57.12300 x,y,z range (A): 53.81000 59.76600 61.11300 scale (grids/A): 2.621374 object centre (A): 8.922000 -34.37100 26.56650 number of atom coordinates read : 2753 total number of charged atoms : 2604 net assigned charge : 6.014014 assigned positive charge : 405.1231 centred at (gu) : 85.90898 87.21396 79.60019 assigned negative charge : -399.1094 centred at (gu) : 86.80042 86.64571 78.85358 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 153001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30428 grid for indexing accessible points = 1.400000 m= 67929 mr = 98031 m= 22712 mr = 49715 m= 4813 mr = 16173 m= 474 mr = 2971 m= 14 mr = 175 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 631 time to turn everything in is 0.8500000 number of dielectric boundary points 81878 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 20824 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) : 1.747582 object centre at (A) : 8.922000 -34.37100 26.56650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9581577E-02 0.2070336 midg,1,midg; midg,igrid,midg 0.4882527 0.4614975 1,midg,midg; igrid,midg,midg 0.1818124 -1.6058241E-04 gauss-seidel spectral radius is 0.9992266 estimated iterations to convergence 284 setup time was (sec) 1.090000 now iterating at: 09:45:19 rms-change max change #iterations 9.368301 302.9584 at 10iterations 5.571949 140.4099 at 20iterations 3.256765 92.13832 at 30iterations 1.895136 47.08893 at 40iterations 1.092432 27.35853 at 50iterations 0.6300004 15.15117 at 60iterations 0.3617664 8.024414 at 70iterations 0.2072921 4.710787 at 80iterations 0.1182863 2.558998 at 90iterations 6.7416385E-02 1.419394 at 100iterations 3.8488321E-02 0.8143711 at 110iterations 2.1929691E-02 0.4287509 at 120iterations 1.2438810E-02 0.2758455 at 130iterations 7.0878034E-03 0.1564035 at 140iterations 4.0192041E-03 8.7442398E-02 at 150iterations 2.2894475E-03 4.8889160E-02 at 160iterations 1.2993786E-03 2.7742386E-02 at 170iterations 7.3929317E-04 1.7171860E-02 at 180iterations finished qdiffx linear iterations at : 09:45:31 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 7.3929317E-04 1.7171860E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 09:45:31 12.720u 0.217s 0:13.29 97.2% 0+0k 0+0io 0pf+0w