Tue Oct 11 06:27:54 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 Tue Oct 11 2011 at 06:27:54 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 = 2025 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: 0.7317274 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): -19.68700 23.83300 ymin,ymax (A): -40.36000 -0.6320001 zmin,zma (A): -36.93000 11.72200 x,y,z range (A): 43.52000 39.72800 48.65200 scale (grids/A): 0.7317274 object centre (A): 2.073000 -20.49600 -12.60400 number of atom coordinates read : 2025 total number of charged atoms : 1899 net assigned charge : 6.500006 assigned positive charge : 306.8871 centred at (gu) : 89.93895 89.38020 91.10735 assigned negative charge : -300.3872 centred at (gu) : 89.77097 89.41853 91.20767 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7574 nv = 96 ne = 84 npr = 40342 no. pairs analyzed = 40342 no. exposed pairs = 2481 no. arc points = 17003 no. surface atoms = 843 nbur = 1182 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 589 mr = 4454 m= 12 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3594 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1489 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4344715E-07 1.7274351E-08 midg,1,midg; midg,igrid,midg 1.4268682E-07 5.8855900E-08 1,midg,midg; igrid,midg,midg -4.1106521E-08 2.2657444E-07 gauss-seidel spectral radius is 0.9902551 estimated iterations to convergence 82 setup time was (sec) 0.5400000 now iterating at: 06:27:54 rms-change max change #iterations 0.2282586 36.77099 at 10iterations 2.9912772E-02 3.747563 at 20iterations 4.1547753E-03 0.5178452 at 30iterations 6.4757839E-04 8.3734393E-02 at 40iterations 1.4854426E-04 2.1245956E-02 at 50iterations finished qdiffx linear iterations at : 06:27:57 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.4854426E-04 2.1245956E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 06:27:58 3.446u 0.161s 0:03.99 90.2% 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 Tue Oct 11 2011 at 06:27:58 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 = 2025 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.195182 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): -19.68700 23.83300 ymin,ymax (A): -40.36000 -0.6320001 zmin,zma (A): -36.93000 11.72200 x,y,z range (A): 43.52000 39.72800 48.65200 scale (grids/A): 2.195182 object centre (A): 2.073000 -20.49600 -12.60400 number of atom coordinates read : 2025 total number of charged atoms : 1899 net assigned charge : 6.500006 assigned positive charge : 306.8871 centred at (gu) : 89.81677 88.14075 93.32196 assigned negative charge : -300.3872 centred at (gu) : 89.31304 88.25568 93.62319 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 79354 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17003 grid for indexing accessible points = 1.400000 m= 33862 mr = 56851 m= 7293 mr = 26138 m= 791 mr = 4935 m= 29 mr = 442 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 32961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 15101 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) : 0.7317274 object centre at (A) : 2.073000 -20.49600 -12.60400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2610610E-02 1.5480316E-02 midg,1,midg; midg,igrid,midg 3.8971011E-02 6.8156943E-03 1,midg,midg; igrid,midg,midg 2.2023497E-02 5.5145070E-02 gauss-seidel spectral radius is 0.9988927 estimated iterations to convergence 238 setup time was (sec) 1.010000 now iterating at: 06:27:59 rms-change max change #iterations 4.767043 188.9729 at 10iterations 2.404815 84.43019 at 20iterations 1.221923 45.56675 at 30iterations 0.6195633 18.76986 at 40iterations 0.3124713 9.763366 at 50iterations 0.1582981 4.452806 at 60iterations 7.9954721E-02 2.407140 at 70iterations 4.0706120E-02 1.217511 at 80iterations 2.0648342E-02 0.6284294 at 90iterations 1.0469714E-02 0.3168793 at 100iterations 5.3593367E-03 0.1548233 at 110iterations 2.7527318E-03 8.2313538E-02 at 120iterations finished qdiffx linear iterations at : 06:28:05 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.7527318E-03 8.2313538E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 06:28:06 7.836u 0.203s 0:08.40 95.5% 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 06:28:06 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 = 2025 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.292773 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): -19.68700 23.83300 ymin,ymax (A): -40.36000 -0.6320001 zmin,zma (A): -36.93000 11.72200 x,y,z range (A): 43.52000 39.72800 48.65200 scale (grids/A): 3.292773 object centre (A): 2.073000 -20.49600 -12.60400 number of atom coordinates read : 2025 total number of charged atoms : 1899 net assigned charge : 6.500006 assigned positive charge : 306.8871 centred at (gu) : 89.72504 87.21101 94.98304 assigned negative charge : -300.3872 centred at (gu) : 88.96965 87.38363 95.43475 start vw surface at 0.1500000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 182807 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17003 grid for indexing accessible points = 1.400000 m= 103304 mr = 136556 m= 44801 mr = 86734 m= 14001 mr = 37276 m= 3087 mr = 10933 m= 420 mr = 2275 m= 18 mr = 291 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.070000 number of dielectric boundary points 74367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 15192 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) : 2.195182 object centre at (A) : 2.073000 -20.49600 -12.60400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3289653 6.8515658E-02 midg,1,midg; midg,igrid,midg 0.2840633 2.7895339E-02 1,midg,midg; igrid,midg,midg 0.4215125 0.4042051 gauss-seidel spectral radius is 0.9993094 estimated iterations to convergence 300 setup time was (sec) 2.400000 now iterating at: 06:28:09 rms-change max change #iterations 10.47836 445.3198 at 10iterations 6.234856 150.1982 at 20iterations 3.697104 68.04231 at 30iterations 2.197872 40.16519 at 40iterations 1.300508 22.63194 at 50iterations 0.7668846 13.30516 at 60iterations 0.4516888 7.841162 at 70iterations 0.2669098 4.751583 at 80iterations 0.1576432 2.684641 at 90iterations 9.2744999E-02 1.647028 at 100iterations 5.4758001E-02 0.9655566 at 110iterations 3.2356564E-02 0.5424051 at 120iterations 1.9272836E-02 0.3739777 at 130iterations 1.1590746E-02 0.2257862 at 140iterations 7.1259155E-03 0.1236618 at 150iterations 4.5307493E-03 7.3574066E-02 at 160iterations 3.0113750E-03 5.4210663E-02 at 170iterations 2.1360181E-03 3.5427094E-02 at 180iterations finished qdiffx linear iterations at : 06:28:20 total time elapsed so far: 13.63000 # loops : 180 mean,max change (kT/e) : 2.1360181E-03 3.5427094E-02 energy calculations done at 13.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.82000 DelPhi exited at 06:28:21 13.822u 0.234s 0:14.37 97.7% 0+0k 0+0io 0pf+0w