Sun Oct 9 07:11:00 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+sph.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 = amb.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 07:11:00 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6580042 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): -13.18200 38.74300 ymin,ymax (A): -22.30600 29.48500 zmin,zma (A): -15.41600 38.68700 x,y,z range (A): 51.92500 51.79100 54.10300 scale (grids/A): 0.6580042 object centre (A): 12.78050 3.589499 11.63550 number of atom coordinates read : 2004 total number of charged atoms : 1819 net assigned charge : 3.000008 assigned positive charge : 288.1011 centred at (gu) : 90.26841 90.28741 89.22253 assigned negative charge : -285.1012 centred at (gu) : 90.37830 90.20796 89.02552 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5852 nv = 96 ne = 84 npr = 41674 no. pairs analyzed = 41674 no. exposed pairs = 2501 no. arc points = 17958 no. surface atoms = 848 nbur = 1156 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 3128 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2600000 number of dielectric boundary points 3009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1731 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6653 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4002810E-08 2.9010875E-08 midg,1,midg; midg,igrid,midg -3.3095076E-09 1.9521618E-08 1,midg,midg; igrid,midg,midg 2.1275797E-08 -8.3159293E-09 gauss-seidel spectral radius is 0.9879778 estimated iterations to convergence 74 setup time was (sec) 0.4700000 now iterating at: 07:11:01 rms-change max change #iterations 0.1384783 21.25265 at 10iterations 1.4529089E-02 2.438240 at 20iterations 1.5268285E-03 0.2598038 at 30iterations 1.6014650E-04 2.4604797E-02 at 40iterations 1.7016986E-05 2.9668808E-03 at 50iterations finished qdiffx linear iterations at : 07:11:03 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 1.7016986E-05 2.9668808E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 07:11:03 3.069u 0.136s 0:03.47 91.9% 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 07:11:03 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.974012 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): -13.18200 38.74300 ymin,ymax (A): -22.30600 29.48500 zmin,zma (A): -15.41600 38.68700 x,y,z range (A): 51.92500 51.79100 54.10300 scale (grids/A): 1.974012 object centre (A): 12.78050 3.589499 11.63550 number of atom coordinates read : 2004 total number of charged atoms : 1819 net assigned charge : 3.000008 assigned positive charge : 288.1011 centred at (gu) : 90.80537 90.86187 87.66740 assigned negative charge : -285.1012 centred at (gu) : 91.13514 90.62390 87.07666 start vw surface at 0.2000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 62219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17958 grid for indexing accessible points = 1.400000 m= 22772 mr = 42112 m= 3591 mr = 16841 m= 192 mr = 2202 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 521 time to turn everything in is 0.5300000 number of dielectric boundary points 27539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 14355 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) : 0.6580042 object centre at (A) : 12.78050 3.589499 11.63550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2954350E-02 2.4196381E-02 midg,1,midg; midg,igrid,midg 1.3454319E-02 4.2163640E-02 1,midg,midg; igrid,midg,midg 1.6665863E-02 -2.5882771E-02 gauss-seidel spectral radius is 0.9986706 estimated iterations to convergence 217 setup time was (sec) 0.8000000 now iterating at: 07:11:04 rms-change max change #iterations 3.843367 163.4706 at 10iterations 1.821275 68.89693 at 20iterations 0.8586570 28.57916 at 30iterations 0.4044876 12.98868 at 40iterations 0.1920708 6.748640 at 50iterations 9.0191901E-02 2.988613 at 60iterations 4.2601127E-02 1.550133 at 70iterations 2.0225726E-02 0.6318531 at 80iterations 9.5301168E-03 0.3119926 at 90iterations 4.5169685E-03 0.1529284 at 100iterations 2.1424573E-03 8.3943844E-02 at 110iterations 1.0104745E-03 3.5183907E-02 at 120iterations finished qdiffx linear iterations at : 07:11:10 total time elapsed so far: 6.690000 # loops : 120 mean,max change (kT/e) : 1.0104745E-03 3.5183907E-02 energy calculations done at 6.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.850000 DelPhi exited at 07:11:11 6.855u 0.186s 0:07.34 95.7% 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 07:11:11 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.961019 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): -13.18200 38.74300 ymin,ymax (A): -22.30600 29.48500 zmin,zma (A): -15.41600 38.68700 x,y,z range (A): 51.92500 51.79100 54.10300 scale (grids/A): 2.961019 object centre (A): 12.78050 3.589499 11.63550 number of atom coordinates read : 2004 total number of charged atoms : 1819 net assigned charge : 3.000008 assigned positive charge : 288.1011 centred at (gu) : 91.20803 91.29298 86.50120 assigned negative charge : -285.1012 centred at (gu) : 91.70272 90.93581 85.61495 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 143525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17958 grid for indexing accessible points = 1.400000 m= 73111 mr = 102087 m= 27068 mr = 59920 m= 6349 mr = 21675 m= 867 mr = 4620 m= 54 mr = 562 m= 0 mr = 34 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 1683 time to turn everything in is 1.140000 number of dielectric boundary points 62076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 14552 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) : 1.974012 object centre at (A) : 12.78050 3.589499 11.63550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5957989 0.2336192 midg,1,midg; midg,igrid,midg 0.2061760 0.4688407 1,midg,midg; igrid,midg,midg 0.2800085 -0.1976073 gauss-seidel spectral radius is 0.9992585 estimated iterations to convergence 290 setup time was (sec) 1.420000 now iterating at: 07:11:12 rms-change max change #iterations 8.821966 427.1875 at 10iterations 5.085271 113.3965 at 20iterations 2.920581 61.52650 at 30iterations 1.680294 31.57885 at 40iterations 0.9640050 21.10909 at 50iterations 0.5539388 10.67370 at 60iterations 0.3167947 7.280932 at 70iterations 0.1813975 3.399609 at 80iterations 0.1042504 2.057566 at 90iterations 5.9737038E-02 1.322380 at 100iterations 3.4251377E-02 0.6723518 at 110iterations 1.9652933E-02 0.3928394 at 120iterations 1.1240264E-02 0.2481022 at 130iterations 6.4538768E-03 0.1358089 at 140iterations 3.7039022E-03 6.9490433E-02 at 150iterations 2.1230630E-03 4.2577028E-02 at 160iterations 1.2145239E-03 2.4477005E-02 at 170iterations 6.9685373E-04 1.4692307E-02 at 180iterations finished qdiffx linear iterations at : 07:11:22 total time elapsed so far: 10.66000 # loops : 180 mean,max change (kT/e) : 6.9685373E-04 1.4692307E-02 energy calculations done at 10.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.84000 DelPhi exited at 07:11:22 10.847u 0.171s 0:11.37 96.8% 0+0k 0+0io 0pf+0w