Sat Oct 15 11:32:29 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 Sat Oct 15 2011 at 11:32:29 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 = 1963 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: 0.6826854 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): 42.62500 94.77200 ymin,ymax (A): -33.49900 6.908000 zmin,zma (A): 81.50900 127.7760 x,y,z range (A): 52.14700 40.40700 46.26701 scale (grids/A): 0.6826854 object centre (A): 68.69850 -13.29550 104.6425 number of atom coordinates read : 1963 total number of charged atoms : 1828 net assigned charge : 1.000006 assigned positive charge : 289.8609 centred at (gu) : 88.33907 88.91624 90.13309 assigned negative charge : -288.8610 centred at (gu) : 88.36742 89.06104 90.11787 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6225 nv = 96 ne = 84 npr = 40586 no. pairs analyzed = 40586 no. exposed pairs = 2516 no. arc points = 17520 no. surface atoms = 842 nbur = 1121 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3397 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1530 ## 113 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6942 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9998954E-11 8.1494411E-09 midg,1,midg; midg,igrid,midg 5.0937441E-08 -2.7031017E-08 1,midg,midg; igrid,midg,midg 1.5842829E-08 -2.2871789E-09 gauss-seidel spectral radius is 0.9888166 estimated iterations to convergence 77 setup time was (sec) 0.5400000 now iterating at: 11:32:30 rms-change max change #iterations 0.1662953 25.25760 at 10iterations 1.9094978E-02 2.805958 at 20iterations 2.2203645E-03 0.3117943 at 30iterations 3.2257085E-04 4.6832085E-02 at 40iterations 7.3384923E-05 1.0564804E-02 at 50iterations finished qdiffx linear iterations at : 11:32:33 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 7.3384923E-05 1.0564804E-02 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 11:32:34 4.083u 0.397s 0:04.98 89.7% 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 Sat Oct 15 2011 at 11:32:34 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 = 1963 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: 2.048056 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): 42.62500 94.77200 ymin,ymax (A): -33.49900 6.908000 zmin,zma (A): 81.50900 127.7760 x,y,z range (A): 52.14700 40.40700 46.26701 scale (grids/A): 2.048056 object centre (A): 68.69850 -13.29550 104.6425 number of atom coordinates read : 1963 total number of charged atoms : 1828 net assigned charge : 1.000006 assigned positive charge : 289.8609 centred at (gu) : 85.01725 86.74854 90.39931 assigned negative charge : -288.8610 centred at (gu) : 85.10243 87.18299 90.35368 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17520 grid for indexing accessible points = 1.400000 m= 25718 mr = 45648 m= 4845 mr = 19094 m= 377 mr = 3068 m= 8 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 29139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 14493 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) : 0.6826854 object centre at (A) : 68.69850 -13.29550 104.6425 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1895702E-03 2.1259133E-02 midg,1,midg; midg,igrid,midg 2.8838867E-02 -1.2011049E-02 1,midg,midg; igrid,midg,midg -3.7011039E-02 -2.4154674E-02 gauss-seidel spectral radius is 0.9987471 estimated iterations to convergence 224 setup time was (sec) 0.8500000 now iterating at: 11:32:35 rms-change max change #iterations 4.177422 178.4304 at 10iterations 2.016893 77.45836 at 20iterations 0.9738386 32.31153 at 30iterations 0.4727123 14.76398 at 40iterations 0.2290416 7.235820 at 50iterations 0.1106037 3.760517 at 60iterations 5.3670470E-02 1.757523 at 70iterations 2.6003199E-02 0.8549919 at 80iterations 1.2558124E-02 0.3724213 at 90iterations 6.1427546E-03 0.1984024 at 100iterations 3.0041991E-03 9.5458984E-02 at 110iterations 1.4819149E-03 4.6299934E-02 at 120iterations finished qdiffx linear iterations at : 11:32:44 total time elapsed so far: 9.620000 # loops : 120 mean,max change (kT/e) : 1.4819149E-03 4.6299934E-02 energy calculations done at 9.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.800000 DelPhi exited at 11:32:45 9.806u 0.471s 0:10.69 96.0% 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 Sat Oct 15 2011 at 11:32:45 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 = 1963 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: 3.072084 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): 42.62500 94.77200 ymin,ymax (A): -33.49900 6.908000 zmin,zma (A): 81.50900 127.7760 x,y,z range (A): 52.14700 40.40700 46.26701 scale (grids/A): 3.072084 object centre (A): 68.69850 -13.29550 104.6425 number of atom coordinates read : 1963 total number of charged atoms : 1828 net assigned charge : 1.000006 assigned positive charge : 289.8609 centred at (gu) : 82.52593 85.12296 90.59907 assigned negative charge : -288.8610 centred at (gu) : 82.65355 85.77452 90.53052 start vw surface at 0.1000000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 152743 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17520 grid for indexing accessible points = 1.400000 m= 80068 mr = 110495 m= 32249 mr = 65620 m= 8999 mr = 25987 m= 1583 mr = 6781 m= 136 mr = 1041 m= 6 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 65788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 14624 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) : 2.048056 object centre at (A) : 68.69850 -13.29550 104.6425 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7894888E-02 0.1497504 midg,1,midg; midg,igrid,midg 0.2538972 -7.9383351E-02 1,midg,midg; igrid,midg,midg -0.4582757 -0.2202998 gauss-seidel spectral radius is 0.9992771 estimated iterations to convergence 293 setup time was (sec) 1.810000 now iterating at: 11:32:47 rms-change max change #iterations 9.567602 393.4174 at 10iterations 5.645063 121.5764 at 20iterations 3.319198 78.78055 at 30iterations 1.945205 39.80861 at 40iterations 1.137720 22.75537 at 50iterations 0.6634675 14.49125 at 60iterations 0.3869053 7.773733 at 70iterations 0.2254061 4.603886 at 80iterations 0.1306217 2.447825 at 90iterations 7.5953320E-02 1.451042 at 100iterations 4.4232510E-02 0.8296937 at 110iterations 2.5626468E-02 0.5091171 at 120iterations 1.4828355E-02 0.2716179 at 130iterations 8.6330613E-03 0.1555009 at 140iterations 5.0170943E-03 0.1011860 at 150iterations 2.9308039E-03 5.2429199E-02 at 160iterations 1.7238812E-03 3.2037735E-02 at 170iterations 1.0283828E-03 1.9741058E-02 at 180iterations finished qdiffx linear iterations at : 11:33:01 total time elapsed so far: 16.17000 # loops : 180 mean,max change (kT/e) : 1.0283828E-03 1.9741058E-02 energy calculations done at 16.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.34000 DelPhi exited at 11:33:02 16.350u 0.502s 0:17.21 97.9% 0+0k 0+0io 0pf+0w