Mon Oct 10 14:25:04 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 14:25:04 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 = 2792 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: 0.5617179 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): 71.11600 124.4030 ymin,ymax (A): 9.452001 72.82900 zmin,zma (A): -8.855000 52.54500 x,y,z range (A): 53.28700 63.37700 61.40000 scale (grids/A): 0.5617179 object centre (A): 97.75950 41.14050 21.84500 number of atom coordinates read : 2792 total number of charged atoms : 2642 net assigned charge : -1.499993 assigned positive charge : 413.0947 centred at (gu) : 88.26152 90.14899 89.45161 assigned negative charge : -414.5956 centred at (gu) : 88.44115 90.24957 89.34802 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5795 nv = 96 ne = 84 npr = 54899 no. pairs analyzed = 54899 no. exposed pairs = 3836 no. arc points = 27396 no. surface atoms = 1289 nbur = 1503 mkacc time = 0.1400000 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 = 1.540000 m= 235 mr = 2740 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2799 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7520 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5378898E-09 8.0719870E-10 midg,1,midg; midg,igrid,midg 8.5978208E-10 -1.3595403E-09 1,midg,midg; igrid,midg,midg 2.6644418E-09 -1.4483502E-09 gauss-seidel spectral radius is 0.9836453 estimated iterations to convergence 64 setup time was (sec) 0.5900000 now iterating at: 14:25:05 rms-change max change #iterations 7.9249732E-02 13.18518 at 10iterations 5.5263154E-03 0.8833542 at 20iterations 3.9581582E-04 7.6274872E-02 at 30iterations 2.8962300E-05 4.6882629E-03 at 40iterations 2.0547241E-06 3.7193298E-04 at 50iterations finished qdiffx linear iterations at : 14:25:09 total time elapsed so far: 4.590000 # loops : 50 mean,max change (kT/e) : 2.0547241E-06 3.7193298E-04 energy calculations done at 4.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 14:25:10 4.771u 0.391s 0:05.64 91.4% 0+0k 0+0io 6pf+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 14:25:10 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 = 2792 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: 1.685154 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): 71.11600 124.4030 ymin,ymax (A): 9.452001 72.82900 zmin,zma (A): -8.855000 52.54500 x,y,z range (A): 53.28700 63.37700 61.40000 scale (grids/A): 1.685154 object centre (A): 97.75950 41.14050 21.84500 number of atom coordinates read : 2792 total number of charged atoms : 2642 net assigned charge : -1.499993 assigned positive charge : 413.0947 centred at (gu) : 84.78397 90.44630 88.35379 assigned negative charge : -414.5956 centred at (gu) : 85.32320 90.74848 88.04373 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27396 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18821 mr = 40694 m= 1894 mr = 12194 m= 57 mr = 743 m= 0 mr = 1 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 30535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 297 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 20396 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) : 0.5617179 object centre at (A) : 97.75950 41.14050 21.84500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6719279E-03 1.4538533E-02 midg,1,midg; midg,igrid,midg 2.3666020E-02 4.4113971E-04 1,midg,midg; igrid,midg,midg 1.1084358E-02 -1.5655877E-02 gauss-seidel spectral radius is 0.9982861 estimated iterations to convergence 192 setup time was (sec) 0.8300000 now iterating at: 14:25:11 rms-change max change #iterations 3.401172 207.7511 at 10iterations 1.443693 66.12773 at 20iterations 0.6168814 26.08078 at 30iterations 0.2623762 10.01981 at 40iterations 0.1116331 4.878574 at 50iterations 4.7546528E-02 1.774296 at 60iterations 2.0369966E-02 0.7016109 at 70iterations 8.6775050E-03 0.3410702 at 80iterations 3.6904227E-03 0.1262681 at 90iterations 1.5786794E-03 6.1357498E-02 at 100iterations 6.7425059E-04 2.4447799E-02 at 110iterations 2.8767606E-04 1.0868549E-02 at 120iterations finished qdiffx linear iterations at : 14:25:21 total time elapsed so far: 10.85000 # loops : 120 mean,max change (kT/e) : 2.8767606E-04 1.0868549E-02 energy calculations done at 10.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.02000 DelPhi exited at 14:25:22 11.026u 0.471s 0:11.99 95.8% 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 Mon Oct 10 2011 at 14:25:22 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 = 2792 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: 2.527731 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): 71.11600 124.4030 ymin,ymax (A): 9.452001 72.82900 zmin,zma (A): -8.855000 52.54500 x,y,z range (A): 53.28700 63.37700 61.40000 scale (grids/A): 2.527731 object centre (A): 97.75950 41.14050 21.84500 number of atom coordinates read : 2792 total number of charged atoms : 2642 net assigned charge : -1.499993 assigned positive charge : 413.0947 centred at (gu) : 82.17587 90.66920 87.53074 assigned negative charge : -414.5956 centred at (gu) : 82.98476 91.12264 87.06554 start vw surface at 0.1200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 147334 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27396 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 64625 mr = 100254 m= 18163 mr = 49255 m= 2684 mr = 12921 m= 204 mr = 1512 m= 5 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 68990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 21126 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) : 1.685154 object centre at (A) : 97.75950 41.14050 21.84500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2206139 0.2152065 midg,1,midg; midg,igrid,midg 0.3827637 -0.1374085 1,midg,midg; igrid,midg,midg 0.1149913 -0.2507370 gauss-seidel spectral radius is 0.9991702 estimated iterations to convergence 274 setup time was (sec) 1.630000 now iterating at: 14:25:24 rms-change max change #iterations 8.682966 314.4736 at 10iterations 4.919439 153.5806 at 20iterations 2.781156 72.14656 at 30iterations 1.560108 40.21753 at 40iterations 0.8757054 19.54400 at 50iterations 0.4876637 10.54141 at 60iterations 0.2718413 6.037069 at 70iterations 0.1515318 3.255722 at 80iterations 8.4143788E-02 1.721130 at 90iterations 4.6742711E-02 0.9837012 at 100iterations 2.6023883E-02 0.5199809 at 110iterations 1.4439118E-02 0.2938089 at 120iterations 8.0043059E-03 0.1778984 at 130iterations 4.4543454E-03 0.1031075 at 140iterations 2.4671569E-03 5.0462246E-02 at 150iterations 1.3695260E-03 2.7329445E-02 at 160iterations 7.6071621E-04 1.7089844E-02 at 170iterations 4.2281783E-04 8.3599091E-03 at 180iterations finished qdiffx linear iterations at : 14:25:40 total time elapsed so far: 17.83000 # loops : 180 mean,max change (kT/e) : 4.2281783E-04 8.3599091E-03 energy calculations done at 17.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.00000 DelPhi exited at 14:25:41 18.008u 0.468s 0:19.00 97.1% 0+0k 0+0io 0pf+0w