Mon Oct 10 17:12:43 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 17:12:43 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 = 2996 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: 0.6156826 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): 14.73000 72.55200 ymin,ymax (A): 3.127000 53.04500 zmin,zma (A): 6.160000 63.70200 x,y,z range (A): 57.82200 49.91800 57.54200 scale (grids/A): 0.6156826 object centre (A): 43.64100 28.08600 34.93100 number of atom coordinates read : 2996 total number of charged atoms : 2854 net assigned charge : -4.499965 assigned positive charge : 449.1618 centred at (gu) : 89.01115 90.53567 91.65130 assigned negative charge : -453.6631 centred at (gu) : 88.96878 90.62802 91.76338 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7598 nv = 96 ne = 84 npr = 59930 no. pairs analyzed = 59930 no. exposed pairs = 3938 no. arc points = 28312 no. surface atoms = 1342 nbur = 1654 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3948 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.3200000 number of dielectric boundary points 4007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2773 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9404 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1406797E-09 -1.5476820E-08 midg,1,midg; midg,igrid,midg 2.8984157E-09 -1.0478272E-08 1,midg,midg; igrid,midg,midg -7.2667210E-09 -8.1906697E-11 gauss-seidel spectral radius is 0.9863822 estimated iterations to convergence 70 setup time was (sec) 0.5400000 now iterating at: 17:12:43 rms-change max change #iterations 0.1300065 18.38915 at 10iterations 1.1657215E-02 1.694832 at 20iterations 1.0633025E-03 0.1721878 at 30iterations 9.7862743E-05 1.4657974E-02 at 40iterations 9.5196747E-06 1.4152527E-03 at 50iterations finished qdiffx linear iterations at : 17:12:46 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 9.5196747E-06 1.4152527E-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 17:12:46 3.141u 0.144s 0:03.66 89.6% 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 17:12:47 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 = 2996 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: 1.847048 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): 14.73000 72.55200 ymin,ymax (A): 3.127000 53.04500 zmin,zma (A): 6.160000 63.70200 x,y,z range (A): 57.82200 49.91800 57.54200 scale (grids/A): 1.847048 object centre (A): 43.64100 28.08600 34.93100 number of atom coordinates read : 2996 total number of charged atoms : 2854 net assigned charge : -4.499965 assigned positive charge : 449.1618 centred at (gu) : 87.03238 91.60594 94.95309 assigned negative charge : -453.6631 centred at (gu) : 86.90607 91.88360 95.28993 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 82294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28312 grid for indexing accessible points = 1.400000 m= 28598 mr = 55112 m= 4151 mr = 20356 m= 207 mr = 2393 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 878 time to turn everything in is 0.5600000 number of dielectric boundary points 37322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 22370 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) : 0.6156826 object centre at (A) : 43.64100 28.08600 34.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1459863E-03 -5.2165207E-03 midg,1,midg; midg,igrid,midg 6.0984571E-03 -2.3734797E-02 1,midg,midg; igrid,midg,midg -5.6220554E-02 9.8318197E-03 gauss-seidel spectral radius is 0.9985976 estimated iterations to convergence 212 setup time was (sec) 0.8400000 now iterating at: 17:12:48 rms-change max change #iterations 4.325894 174.1074 at 10iterations 1.995228 65.12700 at 20iterations 0.9202372 34.64709 at 30iterations 0.4257709 13.65283 at 40iterations 0.1967810 6.633469 at 50iterations 9.1050677E-02 2.761816 at 60iterations 4.2205896E-02 1.364109 at 70iterations 1.9512109E-02 0.6210730 at 80iterations 9.0537993E-03 0.2753201 at 90iterations 4.1823140E-03 0.1259842 at 100iterations 1.9379474E-03 5.7893276E-02 at 110iterations 9.0071640E-04 3.3142090E-02 at 120iterations finished qdiffx linear iterations at : 17:12:54 total time elapsed so far: 6.950000 # loops : 120 mean,max change (kT/e) : 9.0071640E-04 3.3142090E-02 energy calculations done at 6.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.120000 DelPhi exited at 17:12:54 7.127u 0.202s 0:07.79 93.9% 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 17:12:54 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 = 2996 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: 2.770572 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): 14.73000 72.55200 ymin,ymax (A): 3.127000 53.04500 zmin,zma (A): 6.160000 63.70200 x,y,z range (A): 57.82200 49.91800 57.54200 scale (grids/A): 2.770572 object centre (A): 43.64100 28.08600 34.93100 number of atom coordinates read : 2996 total number of charged atoms : 2854 net assigned charge : -4.499965 assigned positive charge : 449.1618 centred at (gu) : 85.54845 92.40868 97.42913 assigned negative charge : -453.6631 centred at (gu) : 85.35902 92.82518 97.93497 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 190061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28312 grid for indexing accessible points = 1.400000 m= 93107 mr = 133913 m= 32326 mr = 74588 m= 7263 mr = 25302 m= 848 mr = 5205 m= 48 mr = 505 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 3129 time to turn everything in is 1.440000 number of dielectric boundary points 84134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 22828 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) : 1.847048 object centre at (A) : 43.64100 28.08600 34.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4579490E-02 0.1929537 midg,1,midg; midg,igrid,midg 7.7936977E-02 -0.2352690 1,midg,midg; igrid,midg,midg -0.7422846 0.1757170 gauss-seidel spectral radius is 0.9992736 estimated iterations to convergence 293 setup time was (sec) 1.730000 now iterating at: 17:12:56 rms-change max change #iterations 10.53249 415.3719 at 10iterations 6.263834 140.4690 at 20iterations 3.695439 83.28165 at 30iterations 2.163071 45.68466 at 40iterations 1.261432 31.95797 at 50iterations 0.7352189 13.93112 at 60iterations 0.4274584 8.820191 at 70iterations 0.2482455 4.986562 at 80iterations 0.1439796 2.684357 at 90iterations 8.3313942E-02 1.634864 at 100iterations 4.8217744E-02 0.8584938 at 110iterations 2.7899396E-02 0.5991199 at 120iterations 1.6134625E-02 0.3088241 at 130iterations 9.3225501E-03 0.1557083 at 140iterations 5.3784577E-03 9.5994949E-02 at 150iterations 3.1111594E-03 5.4799080E-02 at 160iterations 1.7949988E-03 3.2217026E-02 at 170iterations 1.0388405E-03 1.7200470E-02 at 180iterations finished qdiffx linear iterations at : 17:13:07 total time elapsed so far: 12.00000 # loops : 180 mean,max change (kT/e) : 1.0388405E-03 1.7200470E-02 energy calculations done at 12.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 17:13:07 12.183u 0.207s 0:12.85 96.3% 0+0k 0+0io 0pf+0w