Mon Oct 10 14:13:26 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 Mon Oct 10 2011 at 14:13:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2499 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: 0.6456879 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): -123.9590 -76.98600 ymin,ymax (A): 2.642000 57.77700 zmin,zma (A): 28.81100 80.00800 x,y,z range (A): 46.97300 55.13500 51.19700 scale (grids/A): 0.6456879 object centre (A): -100.4725 30.20950 54.40950 number of atom coordinates read : 2499 total number of charged atoms : 2474 net assigned charge : 5.000008 assigned positive charge : 391.0159 centred at (gu) : 89.85002 90.40028 91.43664 assigned negative charge : -386.0164 centred at (gu) : 89.94809 90.49866 91.51762 start vw surface at 0.1400000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7227 nv = 96 ne = 84 npr = 47135 no. pairs analyzed = 47135 no. exposed pairs = 3414 no. arc points = 24315 no. surface atoms = 1143 nbur = 1356 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 428 mr = 3709 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2416 ## 230 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8774 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4510410E-08 -3.2855088E-09 midg,1,midg; midg,igrid,midg 2.0132626E-08 -5.1124562E-09 1,midg,midg; igrid,midg,midg 2.2576716E-08 -4.4416630E-09 gauss-seidel spectral radius is 0.9875718 estimated iterations to convergence 73 setup time was (sec) 0.6500000 now iterating at: 14:13:27 rms-change max change #iterations 0.1491689 20.26324 at 10iterations 1.5117384E-02 2.119383 at 20iterations 1.5304211E-03 0.2208905 at 30iterations 1.5237414E-04 2.0869255E-02 at 40iterations 1.5529937E-05 2.3536682E-03 at 50iterations finished qdiffx linear iterations at : 14:13:31 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 1.5529937E-05 2.3536682E-03 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 14:13:32 4.496u 0.435s 0:05.41 90.9% 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 Mon Oct 10 2011 at 14:13:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2499 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: 1.937064 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): -123.9590 -76.98600 ymin,ymax (A): 2.642000 57.77700 zmin,zma (A): 28.81100 80.00800 x,y,z range (A): 46.97300 55.13500 51.19700 scale (grids/A): 1.937064 object centre (A): -100.4725 30.20950 54.40950 number of atom coordinates read : 2499 total number of charged atoms : 2474 net assigned charge : 5.000008 assigned positive charge : 391.0159 centred at (gu) : 89.54942 91.20026 94.30943 assigned negative charge : -386.0164 centred at (gu) : 89.84399 91.49559 94.55244 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 77203 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24315 grid for indexing accessible points = 1.400000 m= 27997 mr = 51853 m= 4548 mr = 19595 m= 262 mr = 2527 m= 3 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7900000 number of dielectric boundary points 35971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 19496 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) : 0.6456879 object centre at (A) : -100.4725 30.20950 54.40950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7421409E-02 -4.1523222E-03 midg,1,midg; midg,igrid,midg 4.3008655E-02 -2.6645675E-02 1,midg,midg; igrid,midg,midg 2.6385706E-02 -1.1937032E-02 gauss-seidel spectral radius is 0.9986827 estimated iterations to convergence 218 setup time was (sec) 1.120000 now iterating at: 14:13:33 rms-change max change #iterations 4.381272 200.6427 at 10iterations 2.072325 71.87878 at 20iterations 0.9859309 33.71771 at 30iterations 0.4672179 14.35403 at 40iterations 0.2212830 6.873257 at 50iterations 0.1049611 3.183243 at 60iterations 4.9994763E-02 1.602892 at 70iterations 2.3688842E-02 0.7888947 at 80iterations 1.1239585E-02 0.3562584 at 90iterations 5.3582415E-03 0.1887360 at 100iterations 2.5341483E-03 9.8600388E-02 at 110iterations 1.2058747E-03 3.6859989E-02 at 120iterations finished qdiffx linear iterations at : 14:13:43 total time elapsed so far: 10.41000 # loops : 120 mean,max change (kT/e) : 1.2058747E-03 3.6859989E-02 energy calculations done at 10.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.63000 DelPhi exited at 14:13:43 10.634u 0.482s 0:11.59 95.8% 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 14:13:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2499 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: 2.905596 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): -123.9590 -76.98600 ymin,ymax (A): 2.642000 57.77700 zmin,zma (A): 28.81100 80.00800 x,y,z range (A): 46.97300 55.13500 51.19700 scale (grids/A): 2.905596 object centre (A): -100.4725 30.20950 54.40950 number of atom coordinates read : 2499 total number of charged atoms : 2474 net assigned charge : 5.000008 assigned positive charge : 391.0159 centred at (gu) : 89.32402 91.80019 96.46399 assigned negative charge : -386.0164 centred at (gu) : 89.76598 92.24337 96.82854 start vw surface at 0.1600000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 178322 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24315 grid for indexing accessible points = 1.400000 m= 89959 mr = 126471 m= 32683 mr = 71564 m= 8063 mr = 24828 m= 1205 mr = 5590 m= 66 mr = 731 m= 0 mr = 17 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.100000 number of dielectric boundary points 81097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.270000 number of grid points assigned charge 19791 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) : 1.937064 object centre at (A) : -100.4725 30.20950 54.40950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2613217 -9.2835158E-02 midg,1,midg; midg,igrid,midg 0.4946103 -0.5429036 1,midg,midg; igrid,midg,midg 0.2241465 -0.1133615 gauss-seidel spectral radius is 0.9992862 estimated iterations to convergence 295 setup time was (sec) 2.480000 now iterating at: 14:13:46 rms-change max change #iterations 10.41191 374.0434 at 10iterations 6.250173 156.3529 at 20iterations 3.726181 87.79916 at 30iterations 2.209135 52.04543 at 40iterations 1.306593 30.75889 at 50iterations 0.7673258 14.84508 at 60iterations 0.4508034 9.634043 at 70iterations 0.2643211 5.089583 at 80iterations 0.1542983 2.756156 at 90iterations 9.0023525E-02 1.665908 at 100iterations 5.2625865E-02 1.023621 at 110iterations 3.0633472E-02 0.5988617 at 120iterations 1.7860940E-02 0.3564243 at 130iterations 1.0391985E-02 0.1791463 at 140iterations 6.0387305E-03 0.1081181 at 150iterations 3.5283305E-03 6.5208435E-02 at 160iterations 2.0553090E-03 4.2282104E-02 at 170iterations 1.2012003E-03 2.2155762E-02 at 180iterations finished qdiffx linear iterations at : 14:14:02 total time elapsed so far: 18.30000 # loops : 180 mean,max change (kT/e) : 1.2012003E-03 2.2155762E-02 energy calculations done at 18.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.51000 DelPhi exited at 14:14:03 18.515u 0.502s 0:19.50 97.4% 0+0k 0+0io 0pf+0w