Tue Oct 11 08:22:43 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 Tue Oct 11 2011 at 08:22:43 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2717 !!! WARNING: SEP 80 has a net charge of -0.4750 !!! WARNING: HIT 83 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: 0.5762942 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): -18.61000 34.13500 ymin,ymax (A): 38.36700 100.1410 zmin,zma (A): -16.99800 39.80700 x,y,z range (A): 52.74500 61.77400 56.80500 scale (grids/A): 0.5762942 object centre (A): 7.762500 69.25400 11.40450 number of atom coordinates read : 2717 total number of charged atoms : 2568 net assigned charge : 6.039012 assigned positive charge : 417.1317 centred at (gu) : 92.52612 91.89137 90.10690 assigned negative charge : -411.0937 centred at (gu) : 92.58279 91.81825 90.17231 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5833 nv = 96 ne = 84 npr = 54821 no. pairs analyzed = 54821 no. exposed pairs = 3431 no. arc points = 24246 no. surface atoms = 1151 nbur = 1566 mkacc time = 9.9999994E-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 = 1.484000 m= 231 mr = 3022 m= 0 mr = 10 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2485 ## 295 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7516 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2450108E-09 -2.4816871E-11 midg,1,midg; midg,igrid,midg -8.7133273E-11 3.8137262E-09 1,midg,midg; igrid,midg,midg 1.2021214E-09 1.8533995E-10 gauss-seidel spectral radius is 0.9844364 estimated iterations to convergence 66 setup time was (sec) 0.3900000 now iterating at: 08:22:43 rms-change max change #iterations 9.1941565E-02 16.55515 at 10iterations 6.9578849E-03 1.158146 at 20iterations 5.3639355E-04 9.4488144E-02 at 30iterations 4.2266718E-05 7.0037842E-03 at 40iterations 3.2714604E-06 5.0926208E-04 at 50iterations finished qdiffx linear iterations at : 08:22:46 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.2714604E-06 5.0926208E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 08:22:47 3.380u 0.173s 0:04.14 85.7% 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 Tue Oct 11 2011 at 08:22:47 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2717 !!! WARNING: SEP 80 has a net charge of -0.4750 !!! WARNING: HIT 83 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: 1.728883 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): -18.61000 34.13500 ymin,ymax (A): 38.36700 100.1410 zmin,zma (A): -16.99800 39.80700 x,y,z range (A): 52.74500 61.77400 56.80500 scale (grids/A): 1.728883 object centre (A): 7.762500 69.25400 11.40450 number of atom coordinates read : 2717 total number of charged atoms : 2568 net assigned charge : 6.039012 assigned positive charge : 417.1317 centred at (gu) : 97.57781 95.67349 90.32037 assigned negative charge : -411.0937 centred at (gu) : 97.74804 95.45471 90.51686 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24246 grid for indexing accessible points = 1.400000 m= 19824 mr = 43202 m= 2262 mr = 13827 m= 67 mr = 1149 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 553 time to turn everything in is 0.3100000 number of dielectric boundary points 28057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19878 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) : 0.5762942 object centre at (A) : 7.762500 69.25400 11.40450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0294192E-02 -1.0870029E-02 midg,1,midg; midg,igrid,midg -1.0936744E-02 1.3404857E-02 1,midg,midg; igrid,midg,midg -2.7790118E-04 -1.6309181E-03 gauss-seidel spectral radius is 0.9983508 estimated iterations to convergence 195 setup time was (sec) 0.5300000 now iterating at: 08:22:48 rms-change max change #iterations 3.603135 154.2836 at 10iterations 1.563373 57.11079 at 20iterations 0.6794782 26.18206 at 30iterations 0.2941214 10.23433 at 40iterations 0.1275091 5.396103 at 50iterations 5.5317797E-02 1.938347 at 60iterations 2.4000689E-02 0.8063774 at 70iterations 1.0468862E-02 0.4617615 at 80iterations 4.5437478E-03 0.1601715 at 90iterations 1.9666702E-03 6.6770792E-02 at 100iterations 8.5721147E-04 2.9693604E-02 at 110iterations 3.7386391E-04 1.3452530E-02 at 120iterations finished qdiffx linear iterations at : 08:22:55 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 3.7386391E-04 1.3452530E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 08:22:55 7.654u 0.199s 0:08.39 93.4% 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 Tue Oct 11 2011 at 08:22:55 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2717 !!! WARNING: SEP 80 has a net charge of -0.4750 !!! WARNING: HIT 83 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: 2.593324 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): -18.61000 34.13500 ymin,ymax (A): 38.36700 100.1410 zmin,zma (A): -16.99800 39.80700 x,y,z range (A): 52.74500 61.77400 56.80500 scale (grids/A): 2.593324 object centre (A): 7.762500 69.25400 11.40450 number of atom coordinates read : 2717 total number of charged atoms : 2568 net assigned charge : 6.039012 assigned positive charge : 417.1317 centred at (gu) : 101.3667 98.51024 90.48033 assigned negative charge : -411.0937 centred at (gu) : 101.6221 98.18191 90.77534 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 148844 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24246 grid for indexing accessible points = 1.400000 m= 68499 mr = 105710 m= 19865 mr = 54510 m= 3525 mr = 15045 m= 341 mr = 2400 m= 10 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1762 time to turn everything in is 0.7800000 number of dielectric boundary points 63239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 20532 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) : 1.728883 object centre at (A) : 7.762500 69.25400 11.40450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7575784E-02 -0.2641201 midg,1,midg; midg,igrid,midg -0.1464558 6.9613226E-02 1,midg,midg; igrid,midg,midg -4.7678638E-02 -2.3695106E-02 gauss-seidel spectral radius is 0.9991834 estimated iterations to convergence 276 setup time was (sec) 1.020000 now iterating at: 08:22:56 rms-change max change #iterations 8.981546 318.5571 at 10iterations 5.113680 157.6768 at 20iterations 2.892319 71.18330 at 30iterations 1.633902 41.14727 at 40iterations 0.9182535 21.34203 at 50iterations 0.5149606 11.61594 at 60iterations 0.2891021 6.719394 at 70iterations 0.1617369 3.319127 at 80iterations 9.0597451E-02 1.908268 at 90iterations 5.0590906E-02 1.074220 at 100iterations 2.8279195E-02 0.5747910 at 110iterations 1.5821291E-02 0.3449488 at 120iterations 8.8544488E-03 0.1715546 at 130iterations 4.9344371E-03 9.7836256E-02 at 140iterations 2.7508091E-03 5.9801102E-02 at 150iterations 1.5383348E-03 3.1601429E-02 at 160iterations 8.5539714E-04 1.8469334E-02 at 170iterations 4.7760794E-04 1.0559082E-02 at 180iterations finished qdiffx linear iterations at : 08:23:08 total time elapsed so far: 12.09000 # loops : 180 mean,max change (kT/e) : 4.7760794E-04 1.0559082E-02 energy calculations done at 12.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.22000 DelPhi exited at 08:23:08 12.225u 0.202s 0:12.78 97.1% 0+0k 0+0io 0pf+0w