Sat Oct 15 15:12:53 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 Sat Oct 15 2011 at 15:12:53 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 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: 0.6687204 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): -11.96600 36.49800 ymin,ymax (A): 6.963000 55.64800 zmin,zma (A): -7.570000 45.66600 x,y,z range (A): 48.46400 48.68500 53.23600 scale (grids/A): 0.6687204 object centre (A): 12.26600 31.30550 19.04800 number of atom coordinates read : 2783 total number of charged atoms : 2613 net assigned charge : 4.500015 assigned positive charge : 419.7607 centred at (gu) : 90.22131 90.69344 91.49431 assigned negative charge : -415.2613 centred at (gu) : 89.95238 90.56457 91.57083 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8343 nv = 96 ne = 84 npr = 56730 no. pairs analyzed = 56730 no. exposed pairs = 3391 no. arc points = 23416 no. surface atoms = 1135 nbur = 1648 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 539 mr = 4843 m= 2 mr = 78 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 0.2200000 number of dielectric boundary points 3963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2159 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5413053E-08 -8.4141165E-09 midg,1,midg; midg,igrid,midg -1.7152461E-08 5.5309645E-08 1,midg,midg; igrid,midg,midg -5.5707268E-08 8.7195723E-08 gauss-seidel spectral radius is 0.9884208 estimated iterations to convergence 76 setup time was (sec) 0.4200000 now iterating at: 15:12:54 rms-change max change #iterations 0.1824757 21.50757 at 10iterations 2.0500563E-02 2.646976 at 20iterations 2.2219105E-03 0.2784758 at 30iterations 2.5431829E-04 2.9258728E-02 at 40iterations 3.0160603E-05 3.9577484E-03 at 50iterations finished qdiffx linear iterations at : 15:13:00 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 3.0160603E-05 3.9577484E-03 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 15:13:01 3.751u 0.192s 0:07.32 53.8% 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 15 2011 at 15:13:01 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 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: 2.006161 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): -11.96600 36.49800 ymin,ymax (A): 6.963000 55.64800 zmin,zma (A): -7.570000 45.66600 x,y,z range (A): 48.46400 48.68500 53.23600 scale (grids/A): 2.006161 object centre (A): 12.26600 31.30550 19.04800 number of atom coordinates read : 2783 total number of charged atoms : 2613 net assigned charge : 4.500015 assigned positive charge : 419.7607 centred at (gu) : 90.66364 92.08001 94.48245 assigned negative charge : -415.2613 centred at (gu) : 89.85665 91.69335 94.71203 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 89014 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23416 grid for indexing accessible points = 1.400000 m= 35863 mr = 63491 m= 6523 mr = 27238 m= 469 mr = 4311 m= 10 mr = 189 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 36650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 20678 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) : 0.6687204 object centre at (A) : 12.26600 31.30550 19.04800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2409914E-02 -7.5983885E-03 midg,1,midg; midg,igrid,midg -6.7975763E-03 3.5478208E-02 1,midg,midg; igrid,midg,midg -1.8739985E-02 7.5948603E-02 gauss-seidel spectral radius is 0.9987794 estimated iterations to convergence 227 setup time was (sec) 0.7400000 now iterating at: 15:13:02 rms-change max change #iterations 4.919194 340.6447 at 10iterations 2.415079 83.20757 at 20iterations 1.175744 38.70155 at 30iterations 0.5758280 16.23839 at 40iterations 0.2818928 8.724709 at 50iterations 0.1384333 3.977035 at 60iterations 6.7631491E-02 1.878647 at 70iterations 3.3124816E-02 0.9983177 at 80iterations 1.6201694E-02 0.4309006 at 90iterations 7.9395426E-03 0.2093196 at 100iterations 3.8893875E-03 0.1145096 at 110iterations 1.9038871E-03 5.6696892E-02 at 120iterations finished qdiffx linear iterations at : 15:13:13 total time elapsed so far: 8.640000 # loops : 120 mean,max change (kT/e) : 1.9038871E-03 5.6696892E-02 energy calculations done at 8.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.770000 DelPhi exited at 15:13:13 8.772u 0.274s 0:12.63 71.5% 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 Sat Oct 15 2011 at 15:13:13 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.009242 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): -11.96600 36.49800 ymin,ymax (A): 6.963000 55.64800 zmin,zma (A): -7.570000 45.66600 x,y,z range (A): 48.46400 48.68500 53.23600 scale (grids/A): 3.009242 object centre (A): 12.26600 31.30550 19.04800 number of atom coordinates read : 2783 total number of charged atoms : 2613 net assigned charge : 4.500015 assigned positive charge : 419.7607 centred at (gu) : 90.99526 93.11996 96.72349 assigned negative charge : -415.2613 centred at (gu) : 89.78496 92.53997 97.06802 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 205415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23416 grid for indexing accessible points = 1.400000 m= 111419 mr = 152666 m= 45406 mr = 93084 m= 12061 mr = 37450 m= 2029 mr = 9278 m= 145 mr = 1447 m= 4 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 82493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 20904 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) : 2.006161 object centre at (A) : 12.26600 31.30550 19.04800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1102898 0.2799804 midg,1,midg; midg,igrid,midg -9.3565293E-02 0.4183787 1,midg,midg; igrid,midg,midg -0.1544651 0.5707372 gauss-seidel spectral radius is 0.9992947 estimated iterations to convergence 297 setup time was (sec) 1.410000 now iterating at: 15:13:15 rms-change max change #iterations 11.10945 401.5834 at 10iterations 6.531707 122.5293 at 20iterations 3.835011 77.49758 at 30iterations 2.253887 50.37146 at 40iterations 1.320685 26.39178 at 50iterations 0.7729542 12.89267 at 60iterations 0.4521752 7.878221 at 70iterations 0.2649649 4.506634 at 80iterations 0.1544678 2.494499 at 90iterations 9.0344191E-02 1.558338 at 100iterations 5.2903052E-02 0.8072948 at 110iterations 3.0779788E-02 0.4873638 at 120iterations 1.7986521E-02 0.2924128 at 130iterations 1.0540332E-02 0.1749039 at 140iterations 6.1745034E-03 0.1078205 at 150iterations 3.6292875E-03 5.9387207E-02 at 160iterations 2.1540350E-03 3.6666870E-02 at 170iterations 1.2864931E-03 2.3071766E-02 at 180iterations finished qdiffx linear iterations at : 15:13:31 total time elapsed so far: 12.97000 # loops : 180 mean,max change (kT/e) : 1.2864931E-03 2.3071766E-02 energy calculations done at 12.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 15:13:32 13.099u 0.214s 0:18.50 71.8% 0+0k 0+0io 0pf+0w