Sun Oct 9 07:18:09 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 07:18:09 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2511 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5469602 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): -4.363000 42.03300 ymin,ymax (A): 35.80400 88.67599 zmin,zma (A): -3.096000 61.99100 x,y,z range (A): 46.39600 52.87199 65.08700 scale (grids/A): 0.5469602 object centre (A): 18.83500 62.24000 29.44750 number of atom coordinates read : 2511 total number of charged atoms : 2364 net assigned charge : -10.49998 assigned positive charge : 377.7089 centred at (gu) : 90.53025 88.78831 89.45541 assigned negative charge : -388.2093 centred at (gu) : 90.69123 88.45202 89.41312 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4958 nv = 96 ne = 84 npr = 50024 no. pairs analyzed = 50024 no. exposed pairs = 3569 no. arc points = 25404 no. surface atoms = 1195 nbur = 1316 mkacc time = 0.1100000 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 = 1.568000 m= 195 mr = 2308 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2526 ## 332 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6393 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0201442E-09 -3.4067146E-10 midg,1,midg; midg,igrid,midg -3.7180210E-09 9.5153374E-10 1,midg,midg; igrid,midg,midg 2.6600125E-10 -1.8516803E-09 gauss-seidel spectral radius is 0.9827373 estimated iterations to convergence 63 setup time was (sec) 0.5000000 now iterating at: 07:18:10 rms-change max change #iterations 6.5445893E-02 12.01105 at 10iterations 4.2903111E-03 0.9038010 at 20iterations 2.8519655E-04 5.2612305E-02 at 30iterations 1.9277224E-05 4.1637421E-03 at 40iterations 1.4690460E-06 2.5939941E-04 at 50iterations finished qdiffx linear iterations at : 07:18:12 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.4690460E-06 2.5939941E-04 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 07:18:13 3.392u 0.243s 0:03.90 93.0% 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 07:18:13 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2511 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: 1.640881 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): -4.363000 42.03300 ymin,ymax (A): 35.80400 88.67599 zmin,zma (A): -3.096000 61.99100 x,y,z range (A): 46.39600 52.87199 65.08700 scale (grids/A): 1.640881 object centre (A): 18.83500 62.24000 29.44750 number of atom coordinates read : 2511 total number of charged atoms : 2364 net assigned charge : -10.49998 assigned positive charge : 377.7089 centred at (gu) : 91.59026 86.36455 88.36555 assigned negative charge : -388.2093 centred at (gu) : 92.07328 85.35570 88.23897 start vw surface at 0.1500000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 54366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25404 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15878 mr = 34308 m= 1401 mr = 10481 m= 38 mr = 585 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 136 time to turn everything in is 0.4200000 number of dielectric boundary points 26309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 259 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 18101 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) : 0.5469602 object centre at (A) : 18.83500 62.24000 29.44750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3326082E-02 -3.5204152E-03 midg,1,midg; midg,igrid,midg -2.5544075E-02 4.5158253E-03 1,midg,midg; igrid,midg,midg -2.7121301E-03 -1.3404068E-02 gauss-seidel spectral radius is 0.9981551 estimated iterations to convergence 185 setup time was (sec) 0.7100000 now iterating at: 07:18:14 rms-change max change #iterations 3.051601 149.1340 at 10iterations 1.266496 51.68581 at 20iterations 0.5223535 22.50327 at 30iterations 0.2152193 8.853012 at 40iterations 8.8945001E-02 3.388992 at 50iterations 3.6626738E-02 1.561855 at 60iterations 1.5153413E-02 0.6145912 at 70iterations 6.2756608E-03 0.2402039 at 80iterations 2.5926544E-03 0.1076584 at 90iterations 1.0725652E-03 4.0246964E-02 at 100iterations 4.4317148E-04 1.7072678E-02 at 110iterations 1.8339456E-04 7.5664520E-03 at 120iterations finished qdiffx linear iterations at : 07:18:21 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 1.8339456E-04 7.5664520E-03 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 07:18:21 7.600u 0.265s 0:08.12 96.7% 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 07:18:21 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2511 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: 2.461321 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): -4.363000 42.03300 ymin,ymax (A): 35.80400 88.67599 zmin,zma (A): -3.096000 61.99100 x,y,z range (A): 46.39600 52.87199 65.08700 scale (grids/A): 2.461321 object centre (A): 18.83500 62.24000 29.44750 number of atom coordinates read : 2511 total number of charged atoms : 2364 net assigned charge : -10.49998 assigned positive charge : 377.7089 centred at (gu) : 92.38530 84.54673 87.54819 assigned negative charge : -388.2093 centred at (gu) : 93.10979 83.03339 87.35844 start vw surface at 0.1600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 125802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25404 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 55436 mr = 84101 m= 14780 mr = 42741 m= 2070 mr = 10702 m= 125 mr = 1268 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 380 time to turn everything in is 0.9800000 number of dielectric boundary points 59351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 18893 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) : 1.640881 object centre at (A) : 18.83500 62.24000 29.44750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9055790 -5.3407013E-02 midg,1,midg; midg,igrid,midg -0.3377520 8.1680663E-02 1,midg,midg; igrid,midg,midg -3.7870795E-02 -0.1670078 gauss-seidel spectral radius is 0.9991218 estimated iterations to convergence 267 setup time was (sec) 1.290000 now iterating at: 07:18:23 rms-change max change #iterations 8.039176 386.0769 at 10iterations 4.472989 137.7271 at 20iterations 2.494918 78.78848 at 30iterations 1.378296 37.88799 at 40iterations 0.7610311 18.19647 at 50iterations 0.4195980 9.760645 at 60iterations 0.2304215 5.334582 at 70iterations 0.1268634 3.050009 at 80iterations 6.9518782E-02 1.762040 at 90iterations 3.7994288E-02 0.8510451 at 100iterations 2.0833319E-02 0.4694052 at 110iterations 1.1407565E-02 0.2554550 at 120iterations 6.2308321E-03 0.1420755 at 130iterations 3.4143194E-03 8.1382751E-02 at 140iterations 1.8669415E-03 4.1933060E-02 at 150iterations 1.0173386E-03 2.4818420E-02 at 160iterations 5.5606390E-04 1.2363434E-02 at 170iterations 3.0360877E-04 6.4005852E-03 at 180iterations finished qdiffx linear iterations at : 07:18:33 total time elapsed so far: 11.90000 # loops : 180 mean,max change (kT/e) : 3.0360877E-04 6.4005852E-03 energy calculations done at 11.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 07:18:34 12.074u 0.259s 0:12.61 97.7% 0+0k 0+0io 0pf+0w