Sun Oct 16 15:15:09 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 16 2011 at 15:15:09 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2556 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: 0.6476849 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): -56.15800 -1.193000 ymin,ymax (A): -26.75400 24.12600 zmin,zma (A): -2.653000 44.38200 x,y,z range (A): 54.96500 50.88000 47.03500 scale (grids/A): 0.6476849 object centre (A): -28.67550 -1.314000 20.86450 number of atom coordinates read : 2556 total number of charged atoms : 2410 net assigned charge : -2.499996 assigned positive charge : 378.1451 centred at (gu) : 90.58937 90.39639 88.76861 assigned negative charge : -380.6455 centred at (gu) : 90.50199 90.32690 88.60809 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7417 nv = 96 ne = 84 npr = 51799 no. pairs analyzed = 51799 no. exposed pairs = 3180 no. arc points = 22116 no. surface atoms = 1083 nbur = 1473 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 402 mr = 4243 m= 4 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2800000 number of dielectric boundary points 3521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2156 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8647 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5530629E-08 1.3663065E-08 midg,1,midg; midg,igrid,midg -1.2995181E-08 5.8875207E-09 1,midg,midg; igrid,midg,midg -1.4726950E-08 8.9574641E-09 gauss-seidel spectral radius is 0.9876477 estimated iterations to convergence 74 setup time was (sec) 0.4900000 now iterating at: 15:15:10 rms-change max change #iterations 0.1458824 22.25982 at 10iterations 1.4944988E-02 2.311714 at 20iterations 1.5321292E-03 0.2171364 at 30iterations 1.5946290E-04 2.1430969E-02 at 40iterations 1.7366163E-05 2.4185181E-03 at 50iterations finished qdiffx linear iterations at : 15:15:12 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.7366163E-05 2.4185181E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 15:15:12 3.081u 0.157s 0:03.50 92.2% 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 16 2011 at 15:15:13 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2556 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: 1.943055 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): -56.15800 -1.193000 ymin,ymax (A): -26.75400 24.12600 zmin,zma (A): -2.653000 44.38200 x,y,z range (A): 54.96500 50.88000 47.03500 scale (grids/A): 1.943055 object centre (A): -28.67550 -1.314000 20.86450 number of atom coordinates read : 2556 total number of charged atoms : 2410 net assigned charge : -2.499996 assigned positive charge : 378.1451 centred at (gu) : 91.76774 91.18885 86.30547 assigned negative charge : -380.6455 centred at (gu) : 91.50605 90.98045 85.82410 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 79205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22116 grid for indexing accessible points = 1.400000 m= 30354 mr = 55649 m= 5111 mr = 23306 m= 363 mr = 3442 m= 5 mr = 157 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 821 time to turn everything in is 0.5400000 number of dielectric boundary points 32484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19012 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) : 0.6476849 object centre at (A) : -28.67550 -1.314000 20.86450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0695906E-02 2.2536648E-02 midg,1,midg; midg,igrid,midg -4.0575176E-02 -2.7642615E-02 1,midg,midg; igrid,midg,midg -1.6530335E-02 -3.4627732E-02 gauss-seidel spectral radius is 0.9986858 estimated iterations to convergence 219 setup time was (sec) 0.8100000 now iterating at: 15:15:13 rms-change max change #iterations 4.339842 187.3958 at 10iterations 2.072068 69.67751 at 20iterations 0.9822724 31.11989 at 30iterations 0.4676127 15.69917 at 40iterations 0.2224930 7.022625 at 50iterations 0.1056764 3.553826 at 60iterations 5.0233506E-02 1.446068 at 70iterations 2.3995209E-02 0.8296933 at 80iterations 1.1314191E-02 0.3447371 at 90iterations 5.3938143E-03 0.1517200 at 100iterations 2.5793656E-03 9.5680237E-02 at 110iterations 1.2313178E-03 3.5650253E-02 at 120iterations finished qdiffx linear iterations at : 15:15:20 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 1.2313178E-03 3.5650253E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 15:15:20 6.998u 0.169s 0:07.42 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 Sun Oct 16 2011 at 15:15:20 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2556 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: 2.914582 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): -56.15800 -1.193000 ymin,ymax (A): -26.75400 24.12600 zmin,zma (A): -2.653000 44.38200 x,y,z range (A): 54.96500 50.88000 47.03500 scale (grids/A): 2.914582 object centre (A): -28.67550 -1.314000 20.86450 number of atom coordinates read : 2556 total number of charged atoms : 2410 net assigned charge : -2.499996 assigned positive charge : 378.1451 centred at (gu) : 92.65147 91.78307 84.45811 assigned negative charge : -380.6455 centred at (gu) : 92.25890 91.47063 83.73615 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 182838 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22116 grid for indexing accessible points = 1.400000 m= 96691 mr = 134193 m= 37127 mr = 80981 m= 9543 mr = 30791 m= 1588 mr = 7571 m= 101 mr = 1151 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 2762 time to turn everything in is 1.400000 number of dielectric boundary points 73159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 19280 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) : 1.943055 object centre at (A) : -28.67550 -1.314000 20.86450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3763843 0.1611926 midg,1,midg; midg,igrid,midg -0.4943751 -0.3716476 1,midg,midg; igrid,midg,midg -7.7626579E-02 -0.3836346 gauss-seidel spectral radius is 0.9992711 estimated iterations to convergence 292 setup time was (sec) 1.690000 now iterating at: 15:15:22 rms-change max change #iterations 10.05486 384.3170 at 10iterations 5.859282 133.8819 at 20iterations 3.386103 65.87719 at 30iterations 1.962095 44.82595 at 40iterations 1.131320 21.39418 at 50iterations 0.6550550 11.65469 at 60iterations 0.3775660 6.882910 at 70iterations 0.2179786 3.713530 at 80iterations 0.1255587 2.340755 at 90iterations 7.2404385E-02 1.223720 at 100iterations 4.1716203E-02 0.7070999 at 110iterations 2.4074033E-02 0.4162240 at 120iterations 1.3848847E-02 0.2297316 at 130iterations 8.0043515E-03 0.1352768 at 140iterations 4.6241577E-03 8.4497213E-02 at 150iterations 2.6651567E-03 4.4967651E-02 at 160iterations 1.5391768E-03 2.5557041E-02 at 170iterations 8.8680390E-04 1.5197903E-02 at 180iterations finished qdiffx linear iterations at : 15:15:33 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 8.8680390E-04 1.5197903E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 15:15:33 13.033u 0.182s 0:13.47 98.0% 0+0k 0+0io 0pf+0w