Sun Oct 9 11:32:08 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+sph2.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 = amb2.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 Sun Oct 9 2011 at 11:32:09 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: HIR 212 has a net charge of 0.5140 !!! WARNING: CME 459 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of 0.1000 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: 0.5820703 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): -50.48300 10.67800 ymin,ymax (A): -25.15800 25.11900 zmin,zma (A): -28.81000 27.82200 x,y,z range (A): 61.16100 50.27700 56.63200 scale (grids/A): 0.5820703 object centre (A): -19.90250 -1.9499779E-02 -0.4939995 number of atom coordinates read : 3034 total number of charged atoms : 2921 net assigned charge : 5.266016 assigned positive charge : 453.7397 centred at (gu) : 89.52822 91.00031 91.04936 assigned negative charge : -448.4756 centred at (gu) : 89.54299 90.97194 90.99741 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6969 nv = 96 ne = 84 npr = 59240 no. pairs analyzed = 59240 no. exposed pairs = 4087 no. arc points = 28924 no. surface atoms = 1357 nbur = 1677 mkacc time = 0.1200000 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 = 1.484000 m= 346 mr = 3539 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3300000 number of dielectric boundary points 3743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2884 ## 280 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2373168E-11 3.1104637E-09 midg,1,midg; midg,igrid,midg 4.3304688E-10 2.3705420E-09 1,midg,midg; igrid,midg,midg 1.7376306E-09 7.7374634E-10 gauss-seidel spectral radius is 0.9847810 estimated iterations to convergence 67 setup time was (sec) 0.5400000 now iterating at: 11:32:09 rms-change max change #iterations 9.9827960E-02 13.98096 at 10iterations 8.0994209E-03 1.165561 at 20iterations 8.3554292E-04 0.1290512 at 30iterations 1.4209983E-04 2.2377014E-02 at 40iterations 3.2045893E-05 5.0334930E-03 at 50iterations finished qdiffx linear iterations at : 11:32:12 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 3.2045893E-05 5.0334930E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 11:32:12 3.141u 0.150s 0:03.57 92.1% 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 Sun Oct 9 2011 at 11:32:12 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: HIR 212 has a net charge of 0.5140 !!! WARNING: CME 459 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of 0.1000 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: 1.746211 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): -50.48300 10.67800 ymin,ymax (A): -25.15800 25.11900 zmin,zma (A): -28.81000 27.82200 x,y,z range (A): 61.16100 50.27700 56.63200 scale (grids/A): 1.746211 object centre (A): -19.90250 -1.9499779E-02 -0.4939995 number of atom coordinates read : 3034 total number of charged atoms : 2921 net assigned charge : 5.266016 assigned positive charge : 453.7397 centred at (gu) : 88.58337 93.00017 93.14708 assigned negative charge : -448.4756 centred at (gu) : 88.62901 92.91561 92.99203 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 76573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28924 grid for indexing accessible points = 1.400000 m= 25422 mr = 51328 m= 3398 mr = 17465 m= 133 mr = 1788 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 479 time to turn everything in is 0.5100000 number of dielectric boundary points 34928 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 22713 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) : 0.5820703 object centre at (A) : -19.90250 -1.9499779E-02 -0.4939995 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4740504E-03 1.0610107E-02 midg,1,midg; midg,igrid,midg 1.1397726E-02 1.9155497E-02 1,midg,midg; igrid,midg,midg 1.6259901E-02 -3.8301791E-03 gauss-seidel spectral radius is 0.9984478 estimated iterations to convergence 201 setup time was (sec) 0.7700000 now iterating at: 11:32:13 rms-change max change #iterations 3.890929 159.1943 at 10iterations 1.716673 54.12809 at 20iterations 0.7643971 24.93436 at 30iterations 0.3407408 10.60163 at 40iterations 0.1515569 4.753323 at 50iterations 6.7298897E-02 2.241463 at 60iterations 2.9983655E-02 0.9130173 at 70iterations 1.3438804E-02 0.4347348 at 80iterations 5.9759682E-03 0.1809473 at 90iterations 2.6882074E-03 8.9151382E-02 at 100iterations 1.2134856E-03 4.1653290E-02 at 110iterations 5.5045728E-04 1.9741058E-02 at 120iterations finished qdiffx linear iterations at : 11:32:19 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 5.5045728E-04 1.9741058E-02 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 11:32:20 6.960u 0.187s 0:07.42 96.2% 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 Sun Oct 9 2011 at 11:32:20 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: HIR 212 has a net charge of 0.5140 !!! WARNING: CME 459 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of 0.1000 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: 2.619316 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): -50.48300 10.67800 ymin,ymax (A): -25.15800 25.11900 zmin,zma (A): -28.81000 27.82200 x,y,z range (A): 61.16100 50.27700 56.63200 scale (grids/A): 2.619316 object centre (A): -19.90250 -1.9499779E-02 -0.4939995 number of atom coordinates read : 3034 total number of charged atoms : 2921 net assigned charge : 5.266016 assigned positive charge : 453.7397 centred at (gu) : 87.87486 94.50014 94.72052 assigned negative charge : -448.4756 centred at (gu) : 87.94365 94.37348 94.48799 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 177635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28924 grid for indexing accessible points = 1.400000 m= 83964 mr = 125898 m= 27451 mr = 65760 m= 5783 mr = 20751 m= 584 mr = 3940 m= 16 mr = 316 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 1682 time to turn everything in is 1.270000 number of dielectric boundary points 78768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 23364 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) : 1.746211 object centre at (A) : -19.90250 -1.9499779E-02 -0.4939995 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1000898 0.1227521 midg,1,midg; midg,igrid,midg 0.2122162 0.2775206 1,midg,midg; igrid,midg,midg 0.2945191 -9.2511654E-02 gauss-seidel spectral radius is 0.9992244 estimated iterations to convergence 283 setup time was (sec) 1.560000 now iterating at: 11:32:21 rms-change max change #iterations 9.639911 262.6869 at 10iterations 5.627193 173.8597 at 20iterations 3.246964 77.47295 at 30iterations 1.872527 42.21209 at 40iterations 1.073439 23.88895 at 50iterations 0.6142027 14.34747 at 60iterations 0.3504052 6.544441 at 70iterations 0.1997521 4.454500 at 80iterations 0.1135269 2.199158 at 90iterations 6.4821355E-02 1.257476 at 100iterations 3.6777817E-02 0.7142639 at 110iterations 2.0906722E-02 0.4033804 at 120iterations 1.1890020E-02 0.2187605 at 130iterations 6.7551481E-03 0.1309967 at 140iterations 3.8501299E-03 6.8580627E-02 at 150iterations 2.1933452E-03 4.3018341E-02 at 160iterations 1.2542512E-03 2.4429321E-02 at 170iterations 7.2191935E-04 1.3414860E-02 at 180iterations finished qdiffx linear iterations at : 11:32:31 total time elapsed so far: 11.37000 # loops : 180 mean,max change (kT/e) : 7.2191935E-04 1.3414860E-02 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 11:32:32 11.554u 0.164s 0:12.03 97.3% 0+0k 0+0io 0pf+0w