Wed Feb 15 08:55:57 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:58 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 = 2717 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: 0.5762942 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 : 2570 net assigned charge : 6.500021 assigned positive charge : 413.9698 centred at (gu) : 92.51534 91.91297 90.15034 assigned negative charge : -407.4707 centred at (gu) : 92.56986 91.84480 90.22419 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5807 nv = 96 ne = 84 npr = 56130 no. pairs analyzed = 56130 no. exposed pairs = 3408 no. arc points = 24180 no. surface atoms = 1144 nbur = 1573 mkacc time = 0.1100000 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= 232 mr = 3004 m= 0 mr = 12 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2487 ## 294 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7516 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4390188E-09 -7.9874017E-11 midg,1,midg; midg,igrid,midg 3.4690310E-11 3.8168815E-09 1,midg,midg; igrid,midg,midg 1.2299544E-09 4.3068329E-10 gauss-seidel spectral radius is 0.9844356 estimated iterations to convergence 66 setup time was (sec) 0.5100000 now iterating at: 08:55:58 rms-change max change #iterations 8.9520149E-02 16.55408 at 10iterations 6.8165851E-03 1.147537 at 20iterations 5.2279333E-04 8.6822510E-02 at 30iterations 4.1182389E-05 6.5631866E-03 at 40iterations 3.1583952E-06 5.3596497E-04 at 50iterations finished qdiffx linear iterations at : 08:56:01 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 3.1583952E-06 5.3596497E-04 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 08:56:01 3.143u 0.134s 0:04.62 70.7% 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 Wed Feb 15 2012 at 08:56:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2717 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: 1.728883 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 : 2570 net assigned charge : 6.500021 assigned positive charge : 413.9698 centred at (gu) : 97.54551 95.73843 90.45079 assigned negative charge : -407.4707 centred at (gu) : 97.70930 95.53431 90.67253 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 63528 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24180 grid for indexing accessible points = 1.400000 m= 19659 mr = 42670 m= 2252 mr = 13715 m= 65 mr = 1143 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 590 time to turn everything in is 0.5000000 number of dielectric boundary points 27969 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19894 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 1.1407755E-02 -1.0966274E-02 midg,1,midg; midg,igrid,midg -1.0732936E-02 1.3472162E-02 1,midg,midg; igrid,midg,midg -1.6301766E-04 -3.4622021E-04 gauss-seidel spectral radius is 0.9983494 estimated iterations to convergence 195 setup time was (sec) 0.7800000 now iterating at: 08:56:04 rms-change max change #iterations 3.555741 154.2323 at 10iterations 1.542219 57.07253 at 20iterations 0.6697404 26.23237 at 30iterations 0.2903094 9.865120 at 40iterations 0.1257535 4.607088 at 50iterations 5.4459263E-02 1.853888 at 60iterations 2.3658931E-02 0.8267365 at 70iterations 1.0287167E-02 0.3952656 at 80iterations 4.4704564E-03 0.1614170 at 90iterations 1.9370676E-03 7.2217941E-02 at 100iterations 8.4181275E-04 3.0944824E-02 at 110iterations 3.6688626E-04 1.3415813E-02 at 120iterations finished qdiffx linear iterations at : 08:56:10 total time elapsed so far: 6.960000 # loops : 120 mean,max change (kT/e) : 3.6688626E-04 1.3415813E-02 energy calculations done at 6.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 08:56:10 7.149u 0.223s 0:07.80 94.3% 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 Wed Feb 15 2012 at 08:56:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2717 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: 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 : 2570 net assigned charge : 6.500021 assigned positive charge : 413.9698 centred at (gu) : 101.3183 98.60764 90.67594 assigned negative charge : -407.4707 centred at (gu) : 101.5640 98.30131 91.00884 start vw surface at 0.1500000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 147610 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24180 grid for indexing accessible points = 1.400000 m= 67869 mr = 104549 m= 19745 mr = 53970 m= 3502 mr = 14941 m= 345 mr = 2398 m= 10 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 1885 time to turn everything in is 1.150000 number of dielectric boundary points 63043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 20548 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 3.1041620E-02 -0.2648613 midg,1,midg; midg,igrid,midg -0.1449924 7.0468500E-02 1,midg,midg; igrid,midg,midg -4.6253070E-02 -7.8062345E-03 gauss-seidel spectral radius is 0.9991823 estimated iterations to convergence 276 setup time was (sec) 1.460000 now iterating at: 08:56:12 rms-change max change #iterations 8.849874 318.4408 at 10iterations 5.027596 158.6184 at 20iterations 2.835838 74.73730 at 30iterations 1.598903 37.71027 at 40iterations 0.8971130 21.86974 at 50iterations 0.5031303 11.15176 at 60iterations 0.2814587 6.514226 at 70iterations 0.1575882 3.327532 at 80iterations 8.8065647E-02 1.801596 at 90iterations 4.9092960E-02 0.9799747 at 100iterations 2.7433183E-02 0.5735683 at 110iterations 1.5334274E-02 0.3339682 at 120iterations 8.5763233E-03 0.1675904 at 130iterations 4.7696708E-03 0.1055136 at 140iterations 2.6623837E-03 5.6497574E-02 at 150iterations 1.4836282E-03 2.9778779E-02 at 160iterations 8.2605996E-04 1.7124176E-02 at 170iterations 4.6022396E-04 9.4596148E-03 at 180iterations finished qdiffx linear iterations at : 08:56:21 total time elapsed so far: 10.70000 # loops : 180 mean,max change (kT/e) : 4.6022396E-04 9.4596148E-03 energy calculations done at 10.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.86000 DelPhi exited at 08:56:22 10.866u 0.189s 0:11.38 97.0% 0+0k 0+0io 0pf+0w