Tue Oct 11 07:50:52 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 Tue Oct 11 2011 at 07:50:52 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2759 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6386796 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): -13.59500 42.14500 ymin,ymax (A): -22.55300 25.34800 zmin,zma (A): -5.768000 40.32600 x,y,z range (A): 55.74000 47.90100 46.09400 scale (grids/A): 0.6386796 object centre (A): 14.27500 1.397500 17.27900 number of atom coordinates read : 2759 total number of charged atoms : 2395 net assigned charge : 8.500014 assigned positive charge : 384.9170 centred at (gu) : 90.20229 88.93312 89.06849 assigned negative charge : -376.4177 centred at (gu) : 90.21638 88.91536 89.23242 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6748 nv = 96 ne = 84 npr = 51697 no. pairs analyzed = 51697 no. exposed pairs = 3004 no. arc points = 20485 no. surface atoms = 1035 nbur = 1724 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 348 mr = 3822 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2000000 number of dielectric boundary points 3241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2053 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8166 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5791384E-08 -5.1507860E-09 midg,1,midg; midg,igrid,midg 1.2213074E-08 1.0966637E-08 1,midg,midg; igrid,midg,midg 1.2733039E-08 1.0641316E-08 gauss-seidel spectral radius is 0.9872851 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 07:50:53 rms-change max change #iterations 0.1411088 21.23416 at 10iterations 1.4435839E-02 2.178288 at 20iterations 1.7233390E-03 0.2650146 at 30iterations 3.0562218E-04 4.3941498E-02 at 40iterations 7.3503390E-05 1.0969162E-02 at 50iterations finished qdiffx linear iterations at : 07:50:56 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 7.3503390E-05 1.0969162E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 07:50:57 3.345u 0.170s 0:04.18 83.9% 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 Tue Oct 11 2011 at 07:50:57 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2759 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.916039 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): -13.59500 42.14500 ymin,ymax (A): -22.55300 25.34800 zmin,zma (A): -5.768000 40.32600 x,y,z range (A): 55.74000 47.90100 46.09400 scale (grids/A): 1.916039 object centre (A): 14.27500 1.397500 17.27900 number of atom coordinates read : 2759 total number of charged atoms : 2395 net assigned charge : 8.500014 assigned positive charge : 384.9170 centred at (gu) : 90.60648 86.79904 87.20498 assigned negative charge : -376.4177 centred at (gu) : 90.64896 86.74584 87.69711 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20485 grid for indexing accessible points = 1.400000 m= 26831 mr = 51637 m= 3937 mr = 20014 m= 206 mr = 2326 m= 3 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 29897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 151 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18827 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) : 0.6386796 object centre at (A) : 14.27500 1.397500 17.27900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7011979E-02 -4.4165654E-03 midg,1,midg; midg,igrid,midg 1.0548458E-02 2.1530401E-02 1,midg,midg; igrid,midg,midg 2.0989014E-02 2.7815862E-02 gauss-seidel spectral radius is 0.9986352 estimated iterations to convergence 215 setup time was (sec) 0.5900000 now iterating at: 07:50:57 rms-change max change #iterations 4.207058 178.6256 at 10iterations 1.986490 69.11248 at 20iterations 0.9273114 29.32113 at 30iterations 0.4380240 15.57948 at 40iterations 0.2052725 6.538796 at 50iterations 9.6429132E-02 2.948059 at 60iterations 4.5459416E-02 1.396206 at 70iterations 2.1387789E-02 0.6986790 at 80iterations 1.0117338E-02 0.2974358 at 90iterations 4.8173890E-03 0.1510485 at 100iterations 2.3077892E-03 7.9177856E-02 at 110iterations 1.1255506E-03 3.4934998E-02 at 120iterations finished qdiffx linear iterations at : 07:51:05 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 1.1255506E-03 3.4934998E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 07:51:05 7.839u 0.190s 0:08.32 96.3% 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 Tue Oct 11 2011 at 07:51:05 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2759 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.874058 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): -13.59500 42.14500 ymin,ymax (A): -22.55300 25.34800 zmin,zma (A): -5.768000 40.32600 x,y,z range (A): 55.74000 47.90100 46.09400 scale (grids/A): 2.874058 object centre (A): 14.27500 1.397500 17.27900 number of atom coordinates read : 2759 total number of charged atoms : 2395 net assigned charge : 8.500014 assigned positive charge : 384.9170 centred at (gu) : 90.90954 85.19830 85.80741 assigned negative charge : -376.4177 centred at (gu) : 90.97343 85.11874 86.54563 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 168812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20485 grid for indexing accessible points = 1.400000 m= 87030 mr = 124723 m= 30810 mr = 72138 m= 6922 mr = 24770 m= 962 mr = 5013 m= 52 mr = 620 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 67304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 19152 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) : 1.916039 object centre at (A) : 14.27500 1.397500 17.27900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4310581 -0.1081296 midg,1,midg; midg,igrid,midg 7.9626724E-02 0.2386991 1,midg,midg; igrid,midg,midg 9.7013816E-02 0.2153498 gauss-seidel spectral radius is 0.9992479 estimated iterations to convergence 288 setup time was (sec) 1.160000 now iterating at: 07:51:06 rms-change max change #iterations 9.782592 349.8719 at 10iterations 5.679051 144.3838 at 20iterations 3.278370 81.71031 at 30iterations 1.894731 38.17602 at 40iterations 1.090545 19.84873 at 50iterations 0.6269604 11.58660 at 60iterations 0.3593839 6.462798 at 70iterations 0.2064433 4.119667 at 80iterations 0.1182840 2.190281 at 90iterations 6.7808010E-02 1.366497 at 100iterations 3.8832020E-02 0.7100916 at 110iterations 2.2221850E-02 0.4623260 at 120iterations 1.2816453E-02 0.2422714 at 130iterations 7.3639904E-03 0.1315117 at 140iterations 4.2684069E-03 7.6179504E-02 at 150iterations 2.5014102E-03 4.4174194E-02 at 160iterations 1.4941792E-03 2.9977798E-02 at 170iterations 9.1547449E-04 1.9069672E-02 at 180iterations finished qdiffx linear iterations at : 07:51:17 total time elapsed so far: 12.18000 # loops : 180 mean,max change (kT/e) : 9.1547449E-04 1.9069672E-02 energy calculations done at 12.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 07:51:18 12.315u 0.213s 0:12.91 96.9% 0+0k 0+0io 0pf+0w