Mon Oct 10 19:01:27 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 19:01:27 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2780 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5455771 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): 41.25400 106.5060 ymin,ymax (A): 1.799000 54.68000 zmin,zma (A): 1.131000 57.72800 x,y,z range (A): 65.25201 52.88100 56.59700 scale (grids/A): 0.5455771 object centre (A): 73.88000 28.23950 29.42950 number of atom coordinates read : 2780 total number of charged atoms : 2642 net assigned charge : -0.9999820 assigned positive charge : 412.5307 centred at (gu) : 90.99456 89.65498 91.45634 assigned negative charge : -413.5318 centred at (gu) : 90.93584 89.67484 91.51334 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5509 nv = 96 ne = 84 npr = 53171 no. pairs analyzed = 53171 no. exposed pairs = 4184 no. arc points = 29820 no. surface atoms = 1375 nbur = 1405 mkacc time = 0.1800000 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 = 1.568000 m= 273 mr = 2415 m= 0 mr = 13 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3354 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2907 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7053 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9649565E-10 -5.8953115E-10 midg,1,midg; midg,igrid,midg 6.6329782E-11 -1.6574830E-10 1,midg,midg; igrid,midg,midg -3.2686445E-10 3.7919703E-10 gauss-seidel spectral radius is 0.9826788 estimated iterations to convergence 63 setup time was (sec) 0.7000000 now iterating at: 19:01:28 rms-change max change #iterations 6.7771122E-02 11.83991 at 10iterations 4.4853436E-03 0.7736263 at 20iterations 3.3341721E-04 7.8675270E-02 at 30iterations 5.0521245E-05 7.6189041E-03 at 40iterations 1.4727624E-05 2.3927689E-03 at 50iterations finished qdiffx linear iterations at : 19:01:32 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 1.4727624E-05 2.3927689E-03 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 19:01:33 4.537u 0.394s 0:05.50 89.4% 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 Mon Oct 10 2011 at 19:01:33 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2780 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.636731 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): 41.25400 106.5060 ymin,ymax (A): 1.799000 54.68000 zmin,zma (A): 1.131000 57.72800 x,y,z range (A): 65.25201 52.88100 56.59700 scale (grids/A): 1.636731 object centre (A): 73.88000 28.23950 29.42950 number of atom coordinates read : 2780 total number of charged atoms : 2642 net assigned charge : -0.9999820 assigned positive charge : 412.5307 centred at (gu) : 92.98312 88.96416 94.36898 assigned negative charge : -413.5318 centred at (gu) : 92.80762 89.02453 94.53970 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 59602 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29820 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18500 mr = 36645 m= 2330 mr = 11839 m= 65 mr = 1119 m= 0 mr = 7 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 30887 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 273 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20251 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) : 0.5455771 object centre at (A) : 73.88000 28.23950 29.42950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3176020E-03 -6.3956087E-03 midg,1,midg; midg,igrid,midg -5.9400508E-03 -3.7540062E-03 1,midg,midg; igrid,midg,midg 1.8676595E-03 1.5017962E-02 gauss-seidel spectral radius is 0.9981977 estimated iterations to convergence 187 setup time was (sec) 0.9800000 now iterating at: 19:01:34 rms-change max change #iterations 3.179505 162.8115 at 10iterations 1.326752 58.27065 at 20iterations 0.5497847 21.66988 at 30iterations 0.2285967 8.635408 at 40iterations 9.5291369E-02 3.706357 at 50iterations 3.9632913E-02 1.510324 at 60iterations 1.6611284E-02 0.6179810 at 70iterations 6.9351685E-03 0.2552528 at 80iterations 2.8793579E-03 0.1153822 at 90iterations 1.2122123E-03 4.6641111E-02 at 100iterations 5.1486032E-04 1.9861221E-02 at 110iterations 2.2162069E-04 8.1081390E-03 at 120iterations finished qdiffx linear iterations at : 19:01:44 total time elapsed so far: 10.79000 # loops : 120 mean,max change (kT/e) : 2.2162069E-04 8.1081390E-03 energy calculations done at 10.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.99000 DelPhi exited at 19:01:44 10.998u 0.443s 0:11.86 96.3% 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 Mon Oct 10 2011 at 19:01:45 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2780 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: 2.455097 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): 41.25400 106.5060 ymin,ymax (A): 1.799000 54.68000 zmin,zma (A): 1.131000 57.72800 x,y,z range (A): 65.25201 52.88100 56.59700 scale (grids/A): 2.455097 object centre (A): 73.88000 28.23950 29.42950 number of atom coordinates read : 2780 total number of charged atoms : 2642 net assigned charge : -0.9999820 assigned positive charge : 412.5307 centred at (gu) : 94.47430 88.44621 96.55322 assigned negative charge : -413.5318 centred at (gu) : 94.21132 88.53682 96.80959 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 137812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29820 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 61594 mr = 90617 m= 19295 mr = 46039 m= 3717 mr = 13877 m= 295 mr = 2429 m= 5 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.550000 number of dielectric boundary points 69636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 21113 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) : 1.636731 object centre at (A) : 73.88000 28.23950 29.42950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3743003E-02 -0.1160439 midg,1,midg; midg,igrid,midg -9.3141153E-02 -6.0440008E-02 1,midg,midg; igrid,midg,midg 4.5840602E-02 0.2143049 gauss-seidel spectral radius is 0.9991536 estimated iterations to convergence 271 setup time was (sec) 1.900000 now iterating at: 19:01:47 rms-change max change #iterations 8.613315 410.3657 at 10iterations 4.968285 124.4494 at 20iterations 2.837031 75.30343 at 30iterations 1.607053 37.19966 at 40iterations 0.9046030 19.80393 at 50iterations 0.5064983 11.32879 at 60iterations 0.2836502 6.294391 at 70iterations 0.1578784 3.805120 at 80iterations 8.8128731E-02 2.155240 at 90iterations 4.8884086E-02 1.075574 at 100iterations 2.7134450E-02 0.5855770 at 110iterations 1.5077482E-02 0.3202348 at 120iterations 8.3422754E-03 0.1935329 at 130iterations 4.6353368E-03 0.1022024 at 140iterations 2.5661655E-03 6.2051773E-02 at 150iterations 1.4249430E-03 3.0475616E-02 at 160iterations 7.9253846E-04 1.7963409E-02 at 170iterations 4.4214237E-04 1.1074543E-02 at 180iterations finished qdiffx linear iterations at : 19:02:02 total time elapsed so far: 17.08000 # loops : 180 mean,max change (kT/e) : 4.4214237E-04 1.1074543E-02 energy calculations done at 17.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.28000 DelPhi exited at 19:02:03 17.286u 0.495s 0:18.26 97.3% 0+0k 0+0io 0pf+0w