Tue Oct 11 05:55:23 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 Tue Oct 11 2011 at 05:55:23 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: HIR 57 has a net charge of 0.5140 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: 0.7085705 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): -19.87200 27.44800 ymin,ymax (A): -9.950000 28.85500 zmin,zma (A): -3.244000 46.99800 x,y,z range (A): 47.32000 38.80500 50.24200 scale (grids/A): 0.7085705 object centre (A): 3.788000 9.452499 21.87700 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 6.514009 assigned positive charge : 318.2261 centred at (gu) : 89.05936 89.03738 90.67380 assigned negative charge : -311.7121 centred at (gu) : 88.94563 89.05001 90.74566 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7137 nv = 96 ne = 84 npr = 41506 no. pairs analyzed = 41506 no. exposed pairs = 2465 no. arc points = 16996 no. surface atoms = 837 nbur = 1236 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 442 mr = 4154 m= 2 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.3000000 number of dielectric boundary points 3336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1582 ## 128 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7815 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1972210E-08 2.3067827E-08 midg,1,midg; midg,igrid,midg 7.6335866E-08 4.2505057E-08 1,midg,midg; igrid,midg,midg -1.9199580E-09 9.5156906E-08 gauss-seidel spectral radius is 0.9896151 estimated iterations to convergence 80 setup time was (sec) 0.5600000 now iterating at: 05:55:24 rms-change max change #iterations 0.2010898 28.47610 at 10iterations 2.5610415E-02 3.734156 at 20iterations 3.2378873E-03 0.4194641 at 30iterations 4.9408793E-04 8.2571030E-02 at 40iterations 1.1556586E-04 1.9147873E-02 at 50iterations finished qdiffx linear iterations at : 05:55:27 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 1.1556586E-04 1.9147873E-02 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 05:55:28 3.995u 0.265s 0:04.91 86.5% 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 Tue Oct 11 2011 at 05:55:28 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: HIR 57 has a net charge of 0.5140 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: 2.125711 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): -19.87200 27.44800 ymin,ymax (A): -9.950000 28.85500 zmin,zma (A): -3.244000 46.99800 x,y,z range (A): 47.32000 38.80500 50.24200 scale (grids/A): 2.125711 object centre (A): 3.788000 9.452499 21.87700 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 6.514009 assigned positive charge : 318.2261 centred at (gu) : 87.17838 87.11214 92.02151 assigned negative charge : -311.7121 centred at (gu) : 86.83701 87.14997 92.23705 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 75603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16996 grid for indexing accessible points = 1.400000 m= 31055 mr = 54358 m= 6059 mr = 23976 m= 550 mr = 4087 m= 12 mr = 300 m= 0 mr = 6 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 615 time to turn everything in is 0.6900000 number of dielectric boundary points 30552 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15450 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) : 0.7085705 object centre at (A) : 3.788000 9.452499 21.87700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1588314E-02 6.1561987E-02 midg,1,midg; midg,igrid,midg 3.5581250E-02 7.1259928E-03 1,midg,midg; igrid,midg,midg 2.4440918E-02 3.3090867E-02 gauss-seidel spectral radius is 0.9988307 estimated iterations to convergence 231 setup time was (sec) 1.000000 now iterating at: 05:55:29 rms-change max change #iterations 4.620862 178.5391 at 10iterations 2.287388 69.04098 at 20iterations 1.134732 35.52605 at 30iterations 0.5625525 18.81262 at 40iterations 0.2800695 8.701515 at 50iterations 0.1389621 4.469456 at 60iterations 6.8930931E-02 2.046629 at 70iterations 3.4347221E-02 1.043953 at 80iterations 1.7126789E-02 0.5114765 at 90iterations 8.5508842E-03 0.2602448 at 100iterations 4.2755911E-03 0.1274042 at 110iterations 2.1650936E-03 6.4529419E-02 at 120iterations finished qdiffx linear iterations at : 05:55:37 total time elapsed so far: 9.220000 # loops : 120 mean,max change (kT/e) : 2.1650936E-03 6.4529419E-02 energy calculations done at 9.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 05:55:38 9.395u 0.282s 0:10.17 95.0% 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 Tue Oct 11 2011 at 05:55:38 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: HIR 57 has a net charge of 0.5140 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: 3.188567 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): -19.87200 27.44800 ymin,ymax (A): -9.950000 28.85500 zmin,zma (A): -3.244000 46.99800 x,y,z range (A): 47.32000 38.80500 50.24200 scale (grids/A): 3.188567 object centre (A): 3.788000 9.452499 21.87700 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 6.514009 assigned positive charge : 318.2261 centred at (gu) : 85.76751 85.66810 93.03233 assigned negative charge : -311.7121 centred at (gu) : 85.25556 85.72497 93.35565 start vw surface at 0.1400000 fill in re-entrant regions at 0.9700000 boundary points on vw surface= 174378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16996 grid for indexing accessible points = 1.400000 m= 96260 mr = 130795 m= 39618 mr = 80844 m= 11440 mr = 32928 m= 2260 mr = 8933 m= 262 mr = 1704 m= 20 mr = 170 m= 0 mr = 15 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 2046 time to turn everything in is 2.210000 number of dielectric boundary points 68849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.370000 number of grid points assigned charge 15560 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) : 2.125711 object centre at (A) : 3.788000 9.452499 21.87700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3389524 0.9150677 midg,1,midg; midg,igrid,midg 0.2880221 3.8857363E-02 1,midg,midg; igrid,midg,midg 0.4344717 0.2733428 gauss-seidel spectral radius is 0.9992921 estimated iterations to convergence 297 setup time was (sec) 2.540000 now iterating at: 05:55:41 rms-change max change #iterations 10.35142 364.3727 at 10iterations 6.125872 129.8338 at 20iterations 3.613975 82.05052 at 30iterations 2.127967 39.60786 at 40iterations 1.247662 23.24967 at 50iterations 0.7340012 12.88556 at 60iterations 0.4297096 9.283205 at 70iterations 0.2518254 4.435371 at 80iterations 0.1476650 2.785219 at 90iterations 8.6129554E-02 1.579771 at 100iterations 5.0516110E-02 0.8328733 at 110iterations 2.9614786E-02 0.5413876 at 120iterations 1.7442031E-02 0.2907562 at 130iterations 1.0346597E-02 0.1855490 at 140iterations 6.2428280E-03 0.1170540 at 150iterations 3.8625740E-03 7.1631789E-02 at 160iterations 2.4883251E-03 4.3636322E-02 at 170iterations 1.6948943E-03 2.9143333E-02 at 180iterations finished qdiffx linear iterations at : 05:55:55 total time elapsed so far: 16.16000 # loops : 180 mean,max change (kT/e) : 1.6948943E-03 2.9143333E-02 energy calculations done at 16.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.34000 DelPhi exited at 05:55:55 16.343u 0.295s 0:17.11 97.1% 0+0k 0+0io 0pf+0w