Sat Oct 8 12:40:22 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+sph2.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 = amb2.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 Sat Oct 8 2011 at 12:40:22 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6021345 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): -22.37400 17.86400 ymin,ymax (A): -18.07300 31.80400 zmin,zma (A): -76.72800 -17.60500 x,y,z range (A): 40.23800 49.87700 59.12300 scale (grids/A): 0.6021345 object centre (A): -2.255000 6.865499 -47.16650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000008 assigned positive charge : 316.7017 centred at (gu) : 90.06409 89.58859 90.92400 assigned negative charge : -314.7023 centred at (gu) : 90.11704 89.66371 90.69991 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5638 nv = 96 ne = 84 npr = 49570 no. pairs analyzed = 49570 no. exposed pairs = 3141 no. arc points = 22033 no. surface atoms = 1077 nbur = 1250 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 300 mr = 2689 m= 0 mr = 19 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2141 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6939 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1881099E-09 9.5840340E-09 midg,1,midg; midg,igrid,midg 3.5125198E-09 -1.4062658E-09 1,midg,midg; igrid,midg,midg 2.4720661E-09 -8.5267643E-10 gauss-seidel spectral radius is 0.9857107 estimated iterations to convergence 69 setup time was (sec) 0.5900000 now iterating at: 12:40:23 rms-change max change #iterations 9.8741427E-02 16.86921 at 10iterations 9.0529611E-03 1.423855 at 20iterations 1.7853857E-03 0.3319511 at 30iterations 6.9232041E-04 0.1377525 at 40iterations 2.8963515E-04 5.7849884E-02 at 50iterations finished qdiffx linear iterations at : 12:40:26 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 2.8963515E-04 5.7849884E-02 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 12:40:27 4.456u 0.392s 0:05.10 94.9% 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 Sat Oct 8 2011 at 12:40:27 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.806403 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): -22.37400 17.86400 ymin,ymax (A): -18.07300 31.80400 zmin,zma (A): -76.72800 -17.60500 x,y,z range (A): 40.23800 49.87700 59.12300 scale (grids/A): 1.806403 object centre (A): -2.255000 6.865499 -47.16650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000008 assigned positive charge : 316.7017 centred at (gu) : 90.19213 88.76568 92.77187 assigned negative charge : -314.7023 centred at (gu) : 90.35129 88.99129 92.10004 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 61052 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22033 grid for indexing accessible points = 1.400000 m= 19696 mr = 39573 m= 2741 mr = 12619 m= 103 mr = 1457 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 29919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 17183 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) : 0.6021345 object centre at (A) : -2.255000 6.865499 -47.16650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0096188E-02 4.1740056E-02 midg,1,midg; midg,igrid,midg 3.7797168E-03 1.6616590E-04 1,midg,midg; igrid,midg,midg 3.7824919E-03 1.2408332E-03 gauss-seidel spectral radius is 0.9984675 estimated iterations to convergence 203 setup time was (sec) 0.8000000 now iterating at: 12:40:28 rms-change max change #iterations 3.421015 159.9005 at 10iterations 1.522505 55.27728 at 20iterations 0.6787001 26.49636 at 30iterations 0.3052955 11.59678 at 40iterations 0.1365150 4.750057 at 50iterations 6.1037153E-02 2.081015 at 60iterations 2.7754921E-02 0.9750029 at 70iterations 1.2849935E-02 0.4997406 at 80iterations 6.2485687E-03 0.2404728 at 90iterations 3.3031818E-03 0.1389923 at 100iterations 1.9858174E-03 8.6853027E-02 at 110iterations 1.3379646E-03 5.5862427E-02 at 120iterations finished qdiffx linear iterations at : 12:40:38 total time elapsed so far: 10.19000 # loops : 120 mean,max change (kT/e) : 1.3379646E-03 5.5862427E-02 energy calculations done at 10.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.37000 DelPhi exited at 12:40:38 10.375u 0.442s 0:11.07 97.6% 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 Sat Oct 8 2011 at 12:40:38 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.709605 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): -22.37400 17.86400 ymin,ymax (A): -18.07300 31.80400 zmin,zma (A): -76.72800 -17.60500 x,y,z range (A): 40.23800 49.87700 59.12300 scale (grids/A): 2.709605 object centre (A): -2.255000 6.865499 -47.16650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000008 assigned positive charge : 316.7017 centred at (gu) : 90.28822 88.14840 94.15784 assigned negative charge : -314.7023 centred at (gu) : 90.52695 88.48698 93.15006 start vw surface at 0.1000000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 141312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22033 grid for indexing accessible points = 1.400000 m= 64248 mr = 97070 m= 21425 mr = 48857 m= 4618 mr = 15397 m= 494 mr = 3089 m= 20 mr = 292 m= 0 mr = 6 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 67406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 17542 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) : 1.806403 object centre at (A) : -2.255000 6.865499 -47.16650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2033108 0.5901522 midg,1,midg; midg,igrid,midg 2.5802033E-02 -6.8007093E-03 1,midg,midg; igrid,midg,midg 1.8495038E-02 1.8540826E-03 gauss-seidel spectral radius is 0.9992130 estimated iterations to convergence 281 setup time was (sec) 1.620000 now iterating at: 12:40:40 rms-change max change #iterations 8.309621 312.2452 at 10iterations 4.851305 144.9198 at 20iterations 2.787436 65.17216 at 30iterations 1.601006 34.93925 at 40iterations 0.9148713 21.21543 at 50iterations 0.5220211 13.61517 at 60iterations 0.2975933 6.073544 at 70iterations 0.1688155 3.860322 at 80iterations 9.5878445E-02 2.007917 at 90iterations 5.4464050E-02 1.147987 at 100iterations 3.0875335E-02 0.7154846 at 110iterations 1.7563280E-02 0.3684044 at 120iterations 1.0030600E-02 0.2188797 at 130iterations 5.7859696E-03 0.1249352 at 140iterations 3.3913688E-03 8.3702087E-02 at 150iterations 2.0595824E-03 5.2700043E-02 at 160iterations 1.3287771E-03 3.4393311E-02 at 170iterations 9.2517462E-04 2.2991180E-02 at 180iterations finished qdiffx linear iterations at : 12:40:56 total time elapsed so far: 17.34000 # loops : 180 mean,max change (kT/e) : 9.2517462E-04 2.2991180E-02 energy calculations done at 17.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.50000 DelPhi exited at 12:40:56 17.509u 0.481s 0:18.30 98.2% 0+0k 0+0io 0pf+0w