Sat Oct 8 18:13:50 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 Sat Oct 8 2011 at 18:13:50 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3382 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: 0.5306385 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): -9.971999 41.34400 ymin,ymax (A): -39.07700 28.01200 zmin,zma (A): -16.81300 34.04000 x,y,z range (A): 51.31600 67.08900 50.85300 scale (grids/A): 0.5306385 object centre (A): 15.68600 -5.532500 8.613499 number of atom coordinates read : 3382 total number of charged atoms : 3238 net assigned charge : 5.0365925E-06 assigned positive charge : 510.1746 centred at (gu) : 89.83659 91.54771 90.68813 assigned negative charge : -510.1758 centred at (gu) : 89.85281 91.49702 90.65569 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6018 nv = 96 ne = 84 npr = 70219 no. pairs analyzed = 70219 no. exposed pairs = 3891 no. arc points = 26839 no. surface atoms = 1334 nbur = 2048 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 = 1.624000 m= 189 mr = 3336 m= 0 mr = 11 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2701 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 7946 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1903983E-10 1.5692568E-10 midg,1,midg; midg,igrid,midg -1.4788908E-10 3.1047240E-10 1,midg,midg; igrid,midg,midg 6.6094498E-11 -7.0315871E-11 gauss-seidel spectral radius is 0.9817210 estimated iterations to convergence 61 setup time was (sec) 0.4600000 now iterating at: 18:13:51 rms-change max change #iterations 7.0317455E-02 12.72863 at 10iterations 4.4398522E-03 0.7512989 at 20iterations 2.9184466E-04 4.7422409E-02 at 30iterations 2.6099362E-05 4.9018860E-03 at 40iterations 4.4395383E-06 1.0695457E-03 at 50iterations finished qdiffx linear iterations at : 18:13:54 total time elapsed so far: 3.710000 # loops : 50 mean,max change (kT/e) : 4.4395383E-06 1.0695457E-03 energy calculations done at 3.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.840000 DelPhi exited at 18:13:54 3.847u 0.215s 0:04.35 93.1% 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 Sat Oct 8 2011 at 18:13:54 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3382 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: 1.591915 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): -9.971999 41.34400 ymin,ymax (A): -39.07700 28.01200 zmin,zma (A): -16.81300 34.04000 x,y,z range (A): 51.31600 67.08900 50.85300 scale (grids/A): 1.591915 object centre (A): 15.68600 -5.532500 8.613499 number of atom coordinates read : 3382 total number of charged atoms : 3238 net assigned charge : 5.0365925E-06 assigned positive charge : 510.1746 centred at (gu) : 89.50914 94.64244 92.06343 assigned negative charge : -510.1758 centred at (gu) : 89.55793 94.49072 91.96681 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 67245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26839 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19892 mr = 47641 m= 1794 mr = 13738 m= 49 mr = 849 m= 0 mr = 2 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 223 time to turn everything in is 0.3400000 number of dielectric boundary points 26750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 357 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 24633 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) : 0.5306385 object centre at (A) : 15.68600 -5.532500 8.613499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5020850E-03 2.5621769E-03 midg,1,midg; midg,igrid,midg 6.3165566E-03 8.8743214E-03 1,midg,midg; igrid,midg,midg 2.7995615E-03 -1.7243952E-03 gauss-seidel spectral radius is 0.9981094 estimated iterations to convergence 183 setup time was (sec) 0.5900000 now iterating at: 18:13:55 rms-change max change #iterations 3.385617 166.1529 at 10iterations 1.395024 48.97987 at 20iterations 0.5721557 19.83527 at 30iterations 0.2349347 7.664138 at 40iterations 9.6578948E-02 3.787790 at 50iterations 3.9457291E-02 1.471182 at 60iterations 1.6218849E-02 0.5774536 at 70iterations 6.6484693E-03 0.2290449 at 80iterations 2.7449718E-03 9.1572762E-02 at 90iterations 1.1299144E-03 3.6870718E-02 at 100iterations 4.6377684E-04 1.5747070E-02 at 110iterations 1.9203816E-04 6.6013336E-03 at 120iterations finished qdiffx linear iterations at : 18:14:03 total time elapsed so far: 8.540000 # loops : 120 mean,max change (kT/e) : 1.9203816E-04 6.6013336E-03 energy calculations done at 8.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.670000 DelPhi exited at 18:14:04 8.676u 0.259s 0:09.21 96.8% 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 Sat Oct 8 2011 at 18:14:04 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3382 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: 2.387873 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): -9.971999 41.34400 ymin,ymax (A): -39.07700 28.01200 zmin,zma (A): -16.81300 34.04000 x,y,z range (A): 51.31600 67.08900 50.85300 scale (grids/A): 2.387873 object centre (A): 15.68600 -5.532500 8.613499 number of atom coordinates read : 3382 total number of charged atoms : 3238 net assigned charge : 5.0365925E-06 assigned positive charge : 510.1746 centred at (gu) : 89.26327 96.96347 93.09497 assigned negative charge : -510.1758 centred at (gu) : 89.33690 96.73610 92.95004 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 156760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26839 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 71287 mr = 116248 m= 18393 mr = 57193 m= 2773 mr = 13830 m= 164 mr = 1731 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 727 time to turn everything in is 0.8300000 number of dielectric boundary points 60318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 25859 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) : 1.591915 object centre at (A) : 15.68600 -5.532500 8.613499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5005134E-02 5.6196917E-02 midg,1,midg; midg,igrid,midg 0.1732266 0.2109561 1,midg,midg; igrid,midg,midg 5.0495386E-02 -2.1370688E-02 gauss-seidel spectral radius is 0.9991141 estimated iterations to convergence 265 setup time was (sec) 1.080000 now iterating at: 18:14:05 rms-change max change #iterations 8.812796 288.5862 at 10iterations 4.888223 109.1882 at 20iterations 2.697590 62.30949 at 30iterations 1.484394 34.13792 at 40iterations 0.8150751 22.36909 at 50iterations 0.4469057 10.33847 at 60iterations 0.2447730 5.263134 at 70iterations 0.1340731 2.729153 at 80iterations 7.3090859E-02 1.492773 at 90iterations 3.9969977E-02 0.7980223 at 100iterations 2.1775885E-02 0.4114408 at 110iterations 1.1920771E-02 0.2241025 at 120iterations 6.5012048E-03 0.1299949 at 130iterations 3.5491339E-03 7.5305939E-02 at 140iterations 1.9354853E-03 3.8291931E-02 at 150iterations 1.0559961E-03 2.0622969E-02 at 160iterations 5.7702663E-04 1.1343002E-02 at 170iterations 3.1495874E-04 6.4029694E-03 at 180iterations finished qdiffx linear iterations at : 18:14:17 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 3.1495874E-04 6.4029694E-03 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.98000 DelPhi exited at 18:14:17 12.985u 0.209s 0:13.47 97.8% 0+0k 0+0io 0pf+0w