Sun Oct 9 07:45:14 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 07:45:14 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7083732 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): -14.73900 28.29300 ymin,ymax (A): -25.10100 25.15500 zmin,zma (A): -34.55900 8.394000 x,y,z range (A): 43.03200 50.25600 42.95300 scale (grids/A): 0.7083732 object centre (A): 6.777000 2.6999474E-02 -13.08250 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 242.0202 centred at (gu) : 90.04301 88.98090 90.18372 assigned negative charge : -251.5201 centred at (gu) : 90.03587 88.71442 89.80305 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5669 nv = 96 ne = 84 npr = 35040 no. pairs analyzed = 35040 no. exposed pairs = 2072 no. arc points = 14679 no. surface atoms = 696 nbur = 953 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 328 mr = 3130 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 0.1500000 number of dielectric boundary points 2822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1241 ## 83 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6121 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3271224E-07 7.1280532E-08 midg,1,midg; midg,igrid,midg -2.3407672E-07 1.9672534E-08 1,midg,midg; igrid,midg,midg -8.2691912E-08 -7.8189402E-08 gauss-seidel spectral radius is 0.9895756 estimated iterations to convergence 80 setup time was (sec) 0.3600000 now iterating at: 07:45:15 rms-change max change #iterations 0.1827332 29.79323 at 10iterations 2.2431863E-02 3.280746 at 20iterations 2.7112169E-03 0.3893013 at 30iterations 3.3354328E-04 4.7870636E-02 at 40iterations 4.0919578E-05 5.9528351E-03 at 50iterations finished qdiffx linear iterations at : 07:45:18 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 4.0919578E-05 5.9528351E-03 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 07:45:18 3.712u 0.221s 0:04.19 93.7% 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 07:45:19 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.125119 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): -14.73900 28.29300 ymin,ymax (A): -25.10100 25.15500 zmin,zma (A): -34.55900 8.394000 x,y,z range (A): 43.03200 50.25600 42.95300 scale (grids/A): 2.125119 object centre (A): 6.777000 2.6999474E-02 -13.08250 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 242.0202 centred at (gu) : 90.12895 86.94270 90.55123 assigned negative charge : -251.5201 centred at (gu) : 90.10767 86.14319 89.40911 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 59970 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14679 grid for indexing accessible points = 1.400000 m= 22200 mr = 41056 m= 3868 mr = 16685 m= 285 mr = 2518 m= 8 mr = 156 m= 0 mr = 2 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1676 time to turn everything in is 0.3300000 number of dielectric boundary points 25914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 12013 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) : 0.7083732 object centre at (A) : 6.777000 2.6999474E-02 -13.08250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4775301E-02 2.7528560E-02 midg,1,midg; midg,igrid,midg -9.5212996E-02 2.2169095E-02 1,midg,midg; igrid,midg,midg -4.0604554E-02 -4.6215575E-02 gauss-seidel spectral radius is 0.9987953 estimated iterations to convergence 228 setup time was (sec) 0.5800000 now iterating at: 07:45:19 rms-change max change #iterations 4.102178 208.7918 at 10iterations 1.995308 74.29581 at 20iterations 0.9769441 32.25063 at 30iterations 0.4773339 15.63439 at 40iterations 0.2349893 7.503766 at 50iterations 0.1146827 3.545370 at 60iterations 5.5999011E-02 1.877254 at 70iterations 2.7610909E-02 1.032364 at 80iterations 1.3489970E-02 0.4644346 at 90iterations 6.6084634E-03 0.2266682 at 100iterations 3.2407672E-03 0.1093102 at 110iterations 1.5824470E-03 5.1165342E-02 at 120iterations finished qdiffx linear iterations at : 07:45:27 total time elapsed so far: 8.440000 # loops : 120 mean,max change (kT/e) : 1.5824470E-03 5.1165342E-02 energy calculations done at 8.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.580000 DelPhi exited at 07:45:28 8.586u 0.227s 0:09.08 96.9% 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 07:45:28 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.187679 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): -14.73900 28.29300 ymin,ymax (A): -25.10100 25.15500 zmin,zma (A): -34.55900 8.394000 x,y,z range (A): 43.03200 50.25600 42.95300 scale (grids/A): 3.187679 object centre (A): 6.777000 2.6999474E-02 -13.08250 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 242.0202 centred at (gu) : 90.19340 85.41407 90.82684 assigned negative charge : -251.5201 centred at (gu) : 90.16150 84.21487 89.11373 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 138271 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14679 grid for indexing accessible points = 1.400000 m= 70228 mr = 99147 m= 27251 mr = 57781 m= 7068 mr = 22377 m= 1166 mr = 5458 m= 136 mr = 859 m= 7 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 5540 time to turn everything in is 0.9400000 number of dielectric boundary points 58417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 12096 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) : 2.125119 object centre at (A) : 6.777000 2.6999474E-02 -13.08250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5574020 0.3035951 midg,1,midg; midg,igrid,midg -1.050947 0.2994751 1,midg,midg; igrid,midg,midg -0.3014882 -0.3267764 gauss-seidel spectral radius is 0.9992796 estimated iterations to convergence 294 setup time was (sec) 1.200000 now iterating at: 07:45:29 rms-change max change #iterations 9.073193 329.2624 at 10iterations 5.224054 146.6522 at 20iterations 3.016526 60.62599 at 30iterations 1.744245 34.19249 at 40iterations 1.007828 20.59198 at 50iterations 0.5821342 10.48029 at 60iterations 0.3351491 6.216700 at 70iterations 0.1940063 3.632555 at 80iterations 0.1121837 2.427967 at 90iterations 6.4655654E-02 1.235877 at 100iterations 3.7322275E-02 0.6992335 at 110iterations 2.1616695E-02 0.4330902 at 120iterations 1.2475090E-02 0.2371254 at 130iterations 7.1906331E-03 0.1407986 at 140iterations 4.1556433E-03 8.2775116E-02 at 150iterations 2.4036258E-03 4.8382282E-02 at 160iterations 1.3840067E-03 2.9556274E-02 at 170iterations 8.0192846E-04 1.5048981E-02 at 180iterations finished qdiffx linear iterations at : 07:45:41 total time elapsed so far: 13.58000 # loops : 180 mean,max change (kT/e) : 8.0192846E-04 1.5048981E-02 energy calculations done at 13.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.71000 DelPhi exited at 07:45:42 13.716u 0.263s 0:14.49 96.4% 0+0k 0+0io 0pf+0w