Sat Oct 15 14:32:08 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 14:32:08 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 = 4150 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: 0.5329980 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): -2.194000 57.08400 ymin,ymax (A): -5.982000 59.89600 zmin,zma (A): 29.24500 96.03699 x,y,z range (A): 59.27800 65.87800 66.79199 scale (grids/A): 0.5329980 object centre (A): 27.44500 26.95700 62.64100 number of atom coordinates read : 4150 total number of charged atoms : 3999 net assigned charge : -3.999964 assigned positive charge : 637.2716 centred at (gu) : 89.82509 88.75092 90.10949 assigned negative charge : -641.2756 centred at (gu) : 89.93652 88.78091 90.08561 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7761 nv = 96 ne = 84 npr = 78798 no. pairs analyzed = 78798 no. exposed pairs = 6040 no. arc points = 42773 no. surface atoms = 1972 nbur = 2178 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 304 mr = 3569 m= 4 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 4493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4194 ## 548 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 10228 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8302799E-10 -1.2950772E-11 midg,1,midg; midg,igrid,midg 3.4191198E-11 -2.3904695E-10 1,midg,midg; igrid,midg,midg 5.1106680E-10 -7.7439122E-10 gauss-seidel spectral radius is 0.9819660 estimated iterations to convergence 61 setup time was (sec) 0.4600000 now iterating at: 14:32:08 rms-change max change #iterations 7.5722523E-02 11.39981 at 10iterations 4.9444288E-03 0.9417257 at 20iterations 5.5533601E-04 7.4048996E-02 at 30iterations 1.4673377E-04 1.2566566E-02 at 40iterations 4.4961791E-05 3.7803650E-03 at 50iterations finished qdiffx linear iterations at : 14:32:13 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 4.4961791E-05 3.7803650E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 14:32:13 3.547u 0.198s 0:05.73 65.0% 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 Sat Oct 15 2011 at 14:32:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4150 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: 1.598994 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): -2.194000 57.08400 ymin,ymax (A): -5.982000 59.89600 zmin,zma (A): 29.24500 96.03699 x,y,z range (A): 59.27800 65.87800 66.79199 scale (grids/A): 1.598994 object centre (A): 27.44500 26.95700 62.64100 number of atom coordinates read : 4150 total number of charged atoms : 3999 net assigned charge : -3.999964 assigned positive charge : 637.2716 centred at (gu) : 89.47375 86.25142 90.32678 assigned negative charge : -641.2756 centred at (gu) : 89.80927 86.34260 90.25629 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 85442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42773 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 25775 mr = 54533 m= 2503 mr = 16334 m= 68 mr = 956 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 713 time to turn everything in is 0.4300000 number of dielectric boundary points 41965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 446 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 30446 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) : 0.5329980 object centre at (A) : 27.44500 26.95700 62.64100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1141048E-04 -1.2696054E-02 midg,1,midg; midg,igrid,midg 2.3384548E-03 -3.2023508E-03 1,midg,midg; igrid,midg,midg -3.4029182E-04 -1.0386077E-02 gauss-seidel spectral radius is 0.9982558 estimated iterations to convergence 190 setup time was (sec) 0.6600000 now iterating at: 14:32:14 rms-change max change #iterations 3.908482 172.4236 at 10iterations 1.648819 56.73421 at 20iterations 0.6944679 22.42518 at 30iterations 0.2939721 10.41490 at 40iterations 0.1242685 4.327311 at 50iterations 5.2650306E-02 1.644562 at 60iterations 2.2379858E-02 0.8604317 at 70iterations 9.4622523E-03 0.3176794 at 80iterations 4.0543475E-03 0.1374154 at 90iterations 1.7307875E-03 5.9247971E-02 at 100iterations 7.5175537E-04 2.2930622E-02 at 110iterations 3.3538626E-04 1.1116266E-02 at 120iterations finished qdiffx linear iterations at : 14:32:29 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 3.3538626E-04 1.1116266E-02 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.380000 DelPhi exited at 14:32:30 8.386u 0.241s 0:16.73 51.5% 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 14:32:30 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 = 4150 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: 2.398491 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): -2.194000 57.08400 ymin,ymax (A): -5.982000 59.89600 zmin,zma (A): 29.24500 96.03699 x,y,z range (A): 59.27800 65.87800 66.79199 scale (grids/A): 2.398491 object centre (A): 27.44500 26.95700 62.64100 number of atom coordinates read : 4150 total number of charged atoms : 3999 net assigned charge : -3.999964 assigned positive charge : 637.2716 centred at (gu) : 89.21007 84.37668 90.48985 assigned negative charge : -641.2756 centred at (gu) : 89.71387 84.51363 90.38438 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 198596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42773 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 88477 mr = 135059 m= 24670 mr = 66576 m= 3683 mr = 17264 m= 252 mr = 2041 m= 5 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 2189 time to turn everything in is 1.050000 number of dielectric boundary points 94671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 31949 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) : 1.598994 object centre at (A) : 27.44500 26.95700 62.64100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7422924E-02 -0.1877687 midg,1,midg; midg,igrid,midg 0.2386632 1.7286915E-02 1,midg,midg; igrid,midg,midg -1.7535174E-02 -6.0022071E-02 gauss-seidel spectral radius is 0.9992096 estimated iterations to convergence 281 setup time was (sec) 1.320000 now iterating at: 14:32:32 rms-change max change #iterations 10.49232 281.7472 at 10iterations 6.145620 152.0374 at 20iterations 3.575127 85.21519 at 30iterations 2.062072 42.39311 at 40iterations 1.184750 26.42655 at 50iterations 0.6793103 14.71133 at 60iterations 0.3882873 8.275175 at 70iterations 0.2207986 4.695511 at 80iterations 0.1257987 2.567289 at 90iterations 7.1388409E-02 1.395088 at 100iterations 4.0528450E-02 0.8279810 at 110iterations 2.2953952E-02 0.5213547 at 120iterations 1.3002080E-02 0.2713223 at 130iterations 7.3586418E-03 0.1426773 at 140iterations 4.1545345E-03 7.6272964E-02 at 150iterations 2.3534053E-03 4.4584274E-02 at 160iterations 1.3304147E-03 2.6920319E-02 at 170iterations 7.5070973E-04 1.3621807E-02 at 180iterations finished qdiffx linear iterations at : 14:32:57 total time elapsed so far: 13.77000 # loops : 180 mean,max change (kT/e) : 7.5070973E-04 1.3621807E-02 energy calculations done at 13.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.90000 DelPhi exited at 14:32:58 13.905u 0.244s 0:27.95 50.5% 0+0k 0+0io 0pf+0w