Mon Oct 10 23:54:00 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 Mon Oct 10 2011 at 23:54:00 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 0.5781849 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): 13.95000 67.80500 ymin,ymax (A): 16.11500 77.68700 zmin,zma (A): 23.13800 64.63500 x,y,z range (A): 53.85500 61.57200 41.49700 scale (grids/A): 0.5781849 object centre (A): 40.87750 46.90100 43.88650 number of atom coordinates read : 2577 total number of charged atoms : 2432 net assigned charge : 4.906014 assigned positive charge : 385.1898 centred at (gu) : 89.07500 89.12981 90.08295 assigned negative charge : -380.2845 centred at (gu) : 89.00872 89.31469 89.96680 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5630 nv = 96 ne = 84 npr = 52791 no. pairs analyzed = 52791 no. exposed pairs = 2977 no. arc points = 20965 no. surface atoms = 1003 nbur = 1574 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 = 1.484000 m= 222 mr = 3147 m= 0 mr = 19 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.3000000 number of dielectric boundary points 2686 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2105 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7145 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0755647E-09 3.0768139E-09 midg,1,midg; midg,igrid,midg 5.1535780E-09 -1.9098654E-09 1,midg,midg; igrid,midg,midg -2.5770100E-10 1.7366882E-09 gauss-seidel spectral radius is 0.9845236 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 23:54:01 rms-change max change #iterations 9.3678363E-02 14.71912 at 10iterations 7.9671964E-03 1.278557 at 20iterations 1.0428404E-03 0.2268562 at 30iterations 2.2708776E-04 5.5229187E-02 at 40iterations 5.5819070E-05 1.3801575E-02 at 50iterations finished qdiffx linear iterations at : 23:54:04 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 5.5819070E-05 1.3801575E-02 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 23:54:05 4.420u 0.384s 0:05.59 85.8% 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 23:54:05 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 1.734555 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): 13.95000 67.80500 ymin,ymax (A): 16.11500 77.68700 zmin,zma (A): 23.13800 64.63500 x,y,z range (A): 53.85500 61.57200 41.49700 scale (grids/A): 1.734555 object centre (A): 40.87750 46.90100 43.88650 number of atom coordinates read : 2577 total number of charged atoms : 2432 net assigned charge : 4.906014 assigned positive charge : 385.1898 centred at (gu) : 87.22456 87.38877 90.24829 assigned negative charge : -380.2845 centred at (gu) : 87.02587 87.94392 89.90004 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 62321 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20965 grid for indexing accessible points = 1.400000 m= 20468 mr = 43906 m= 2495 mr = 15062 m= 67 mr = 1484 m= 0 mr = 6 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2749 time to turn everything in is 0.4900000 number of dielectric boundary points 24893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 18859 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) : 0.5781849 object centre at (A) : 40.87750 46.90100 43.88650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5934332E-03 1.4186391E-02 midg,1,midg; midg,igrid,midg -7.7121002E-03 -2.4344230E-02 1,midg,midg; igrid,midg,midg 1.4633565E-03 1.3555025E-02 gauss-seidel spectral radius is 0.9983498 estimated iterations to convergence 195 setup time was (sec) 0.8300000 now iterating at: 23:54:07 rms-change max change #iterations 3.490356 168.4903 at 10iterations 1.511724 54.57535 at 20iterations 0.6567427 24.33501 at 30iterations 0.2859620 11.01621 at 40iterations 0.1240288 4.860449 at 50iterations 5.3983461E-02 1.996201 at 60iterations 2.3682352E-02 0.8084221 at 70iterations 1.0458867E-02 0.4256859 at 80iterations 4.6944432E-03 0.1918793 at 90iterations 2.1680722E-03 9.0824127E-02 at 100iterations 1.0732502E-03 4.7618866E-02 at 110iterations 5.7154917E-04 2.5325775E-02 at 120iterations finished qdiffx linear iterations at : 23:54:16 total time elapsed so far: 9.980000 # loops : 120 mean,max change (kT/e) : 5.7154917E-04 2.5325775E-02 energy calculations done at 9.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.15000 DelPhi exited at 23:54:17 10.152u 0.452s 0:11.16 94.9% 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 23:54:17 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 2.601832 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): 13.95000 67.80500 ymin,ymax (A): 16.11500 77.68700 zmin,zma (A): 23.13800 64.63500 x,y,z range (A): 53.85500 61.57200 41.49700 scale (grids/A): 2.601832 object centre (A): 40.87750 46.90100 43.88650 number of atom coordinates read : 2577 total number of charged atoms : 2432 net assigned charge : 4.906014 assigned positive charge : 385.1898 centred at (gu) : 85.83653 86.08311 90.37228 assigned negative charge : -380.2845 centred at (gu) : 85.53876 86.91579 89.85000 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 144678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20965 grid for indexing accessible points = 1.400000 m= 69667 mr = 106622 m= 21881 mr = 57346 m= 4196 mr = 17419 m= 335 mr = 3135 m= 8 mr = 187 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 9192 time to turn everything in is 1.270000 number of dielectric boundary points 56056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 19441 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) : 1.734555 object centre at (A) : 40.87750 46.90100 43.88650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4774968E-02 0.1779365 midg,1,midg; midg,igrid,midg -0.4217969 -0.3050245 1,midg,midg; igrid,midg,midg 1.9697491E-03 0.1311977 gauss-seidel spectral radius is 0.9991704 estimated iterations to convergence 274 setup time was (sec) 1.610000 now iterating at: 23:54:19 rms-change max change #iterations 8.452136 343.5541 at 10iterations 4.737041 114.1558 at 20iterations 2.643906 59.52053 at 30iterations 1.474592 33.17654 at 40iterations 0.8192165 17.67705 at 50iterations 0.4563446 10.08677 at 60iterations 0.2542782 5.518978 at 70iterations 0.1410968 3.251297 at 80iterations 7.8483395E-02 1.801392 at 90iterations 4.3570492E-02 0.9265289 at 100iterations 2.4306988E-02 0.5039201 at 110iterations 1.3519898E-02 0.3016281 at 120iterations 7.5761941E-03 0.1569691 at 130iterations 4.2380071E-03 9.2639923E-02 at 140iterations 2.3916853E-03 4.9037933E-02 at 150iterations 1.3800139E-03 3.3580780E-02 at 160iterations 8.1739284E-04 2.1087646E-02 at 170iterations 5.0207932E-04 1.3698578E-02 at 180iterations finished qdiffx linear iterations at : 23:54:34 total time elapsed so far: 16.61000 # loops : 180 mean,max change (kT/e) : 5.0207932E-04 1.3698578E-02 energy calculations done at 16.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.76000 DelPhi exited at 23:54:34 16.768u 0.470s 0:17.51 98.4% 0+0k 0+0io 0pf+0w