Mon Oct 10 14:01:31 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 14:01:31 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 = 2495 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: 0.6766773 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): 34.38000 83.06500 ymin,ymax (A): -6.175000 41.94400 zmin,zma (A): 68.07700 120.6870 x,y,z range (A): 48.68501 48.11900 52.61001 scale (grids/A): 0.6766773 object centre (A): 58.72250 17.88450 94.38200 number of atom coordinates read : 2495 total number of charged atoms : 2357 net assigned charge : 6.000014 assigned positive charge : 374.3480 centred at (gu) : 89.60749 90.51028 89.42753 assigned negative charge : -368.3485 centred at (gu) : 89.54284 90.44426 89.29510 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7775 nv = 96 ne = 84 npr = 50256 no. pairs analyzed = 50256 no. exposed pairs = 3258 no. arc points = 22738 no. surface atoms = 1097 nbur = 1398 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 522 mr = 4165 m= 4 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2020 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8860 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6296740E-08 5.4448606E-08 midg,1,midg; midg,igrid,midg 4.6348698E-09 4.7231477E-08 1,midg,midg; igrid,midg,midg 5.7418585E-09 3.9029224E-08 gauss-seidel spectral radius is 0.9886729 estimated iterations to convergence 77 setup time was (sec) 0.5100000 now iterating at: 14:01:32 rms-change max change #iterations 0.1856711 24.35165 at 10iterations 2.0872252E-02 2.995541 at 20iterations 2.7478095E-03 0.3853865 at 30iterations 6.6492887E-04 9.4152451E-02 at 40iterations 2.6100231E-04 3.7389755E-02 at 50iterations finished qdiffx linear iterations at : 14:01:34 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 2.6100231E-04 3.7389755E-02 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 14:01:36 3.115u 0.157s 0:04.23 77.0% 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 Mon Oct 10 2011 at 14:01:36 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 = 2495 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.030032 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): 34.38000 83.06500 ymin,ymax (A): -6.175000 41.94400 zmin,zma (A): 68.07700 120.6870 x,y,z range (A): 48.68501 48.11900 52.61001 scale (grids/A): 2.030032 object centre (A): 58.72250 17.88450 94.38200 number of atom coordinates read : 2495 total number of charged atoms : 2357 net assigned charge : 6.000014 assigned positive charge : 374.3480 centred at (gu) : 88.82213 91.53059 88.28186 assigned negative charge : -368.3485 centred at (gu) : 88.62843 91.33254 87.88502 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 81351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22738 grid for indexing accessible points = 1.400000 m= 31877 mr = 55163 m= 6311 mr = 23199 m= 535 mr = 3928 m= 16 mr = 285 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 37515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 18655 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) : 0.6766773 object centre at (A) : 58.72250 17.88450 94.38200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1928744E-02 4.2756882E-02 midg,1,midg; midg,igrid,midg -9.1488315E-03 4.3544665E-02 1,midg,midg; igrid,midg,midg 3.2527680E-03 1.2408303E-02 gauss-seidel spectral radius is 0.9987909 estimated iterations to convergence 228 setup time was (sec) 0.9700000 now iterating at: 14:01:37 rms-change max change #iterations 4.717964 211.3182 at 10iterations 2.310900 74.59193 at 20iterations 1.133796 36.18443 at 30iterations 0.5567160 18.10782 at 40iterations 0.2728696 8.654961 at 50iterations 0.1336911 3.848289 at 60iterations 6.5741375E-02 1.905378 at 70iterations 3.2328926E-02 1.103767 at 80iterations 1.5921667E-02 0.4842415 at 90iterations 7.9380916E-03 0.2378750 at 100iterations 4.0291711E-03 0.1131783 at 110iterations 2.1179256E-03 6.8227768E-02 at 120iterations finished qdiffx linear iterations at : 14:01:43 total time elapsed so far: 7.070000 # loops : 120 mean,max change (kT/e) : 2.1179256E-03 6.8227768E-02 energy calculations done at 7.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.240000 DelPhi exited at 14:01:44 7.244u 0.188s 0:08.53 86.9% 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 Mon Oct 10 2011 at 14:01:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2495 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: 3.045048 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): 34.38000 83.06500 ymin,ymax (A): -6.175000 41.94400 zmin,zma (A): 68.07700 120.6870 x,y,z range (A): 48.68501 48.11900 52.61001 scale (grids/A): 3.045048 object centre (A): 58.72250 17.88450 94.38200 number of atom coordinates read : 2495 total number of charged atoms : 2357 net assigned charge : 6.000014 assigned positive charge : 374.3480 centred at (gu) : 88.23302 92.29560 87.42267 assigned negative charge : -368.3485 centred at (gu) : 87.94251 91.99880 86.82751 start vw surface at 0.1900000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 187133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22738 grid for indexing accessible points = 1.400000 m= 97983 mr = 133413 m= 40891 mr = 79055 m= 11812 mr = 32612 m= 2189 mr = 8814 m= 287 mr = 1549 m= 11 mr = 198 m= 0 mr = 2 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.650000 number of dielectric boundary points 84663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 18856 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) : 2.030032 object centre at (A) : 58.72250 17.88450 94.38200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6729804E-02 0.4253140 midg,1,midg; midg,igrid,midg -7.5815901E-02 0.4050179 1,midg,midg; igrid,midg,midg -7.6550700E-02 3.4765985E-02 gauss-seidel spectral radius is 0.9993093 estimated iterations to convergence 300 setup time was (sec) 1.980000 now iterating at: 14:01:47 rms-change max change #iterations 10.91219 384.5872 at 10iterations 6.576715 140.8903 at 20iterations 3.960180 87.71288 at 30iterations 2.366132 56.43030 at 40iterations 1.408172 33.06620 at 50iterations 0.8371669 15.36663 at 60iterations 0.4957445 9.111095 at 70iterations 0.2931733 5.696509 at 80iterations 0.1729597 3.079819 at 90iterations 0.1021621 1.811035 at 100iterations 6.0063232E-02 0.9852715 at 110iterations 3.5357781E-02 0.5787594 at 120iterations 2.0820977E-02 0.3738365 at 130iterations 1.2263086E-02 0.2102938 at 140iterations 7.2616269E-03 0.1416855 at 150iterations 4.3195053E-03 7.2276115E-02 at 160iterations 2.6003742E-03 4.5147896E-02 at 170iterations 1.6024994E-03 2.9592514E-02 at 180iterations finished qdiffx linear iterations at : 14:01:58 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 1.6024994E-03 2.9592514E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.14000 DelPhi exited at 14:01:59 13.146u 0.237s 0:14.42 92.7% 0+0k 0+0io 0pf+0w