Mon Oct 10 17:03:34 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 17:03:34 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 = 2966 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: 0.5505041 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): -34.44700 30.22100 ymin,ymax (A): -21.20900 25.66200 zmin,zma (A): -40.26100 6.759000 x,y,z range (A): 64.66800 46.87100 47.02000 scale (grids/A): 0.5505041 object centre (A): -2.113002 2.226500 -16.75100 number of atom coordinates read : 2966 total number of charged atoms : 2825 net assigned charge : -3.499968 assigned positive charge : 442.6930 centred at (gu) : 89.58595 90.22215 90.67262 assigned negative charge : -446.1941 centred at (gu) : 89.52787 90.07584 90.74175 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5772 nv = 96 ne = 84 npr = 59830 no. pairs analyzed = 59830 no. exposed pairs = 3846 no. arc points = 26829 no. surface atoms = 1304 nbur = 1662 mkacc time = 0.1400000 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= 208 mr = 2849 m= 0 mr = 11 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2782 ## 332 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3980226E-10 -9.5103991E-10 midg,1,midg; midg,igrid,midg -1.3540910E-09 9.2898883E-10 1,midg,midg; igrid,midg,midg -7.9368701E-10 1.7898420E-10 gauss-seidel spectral radius is 0.9829863 estimated iterations to convergence 63 setup time was (sec) 0.6000000 now iterating at: 17:03:34 rms-change max change #iterations 7.3781431E-02 14.97873 at 10iterations 5.0473865E-03 0.8659821 at 20iterations 3.3820682E-04 5.0729752E-02 at 30iterations 2.3694110E-05 4.1027069E-03 at 40iterations 1.5873862E-06 2.5558472E-04 at 50iterations finished qdiffx linear iterations at : 17:03:38 total time elapsed so far: 3.700000 # loops : 50 mean,max change (kT/e) : 1.5873862E-06 2.5558472E-04 energy calculations done at 3.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 17:03:39 3.936u 0.205s 0:05.82 70.9% 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 17:03:39 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 = 2966 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: 1.651512 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): -34.44700 30.22100 ymin,ymax (A): -21.20900 25.66200 zmin,zma (A): -40.26100 6.759000 x,y,z range (A): 64.66800 46.87100 47.02000 scale (grids/A): 1.651512 object centre (A): -2.113002 2.226500 -16.75100 number of atom coordinates read : 2966 total number of charged atoms : 2825 net assigned charge : -3.499968 assigned positive charge : 442.6930 centred at (gu) : 88.75711 90.66554 92.01703 assigned negative charge : -446.1941 centred at (gu) : 88.58323 90.22733 92.22466 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 64414 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26829 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18495 mr = 42864 m= 1790 mr = 12283 m= 44 mr = 754 m= 0 mr = 2 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 133 time to turn everything in is 0.5200000 number of dielectric boundary points 28840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 331 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 21699 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) : 0.5505041 object centre at (A) : -2.113002 2.226500 -16.75100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3663230E-03 -5.4871286E-03 midg,1,midg; midg,igrid,midg -1.6098520E-02 9.3831839E-03 1,midg,midg; igrid,midg,midg -2.1300299E-02 7.0376485E-04 gauss-seidel spectral radius is 0.9982253 estimated iterations to convergence 189 setup time was (sec) 0.8300000 now iterating at: 17:03:40 rms-change max change #iterations 3.396665 160.9402 at 10iterations 1.417637 54.52333 at 20iterations 0.5963139 23.55833 at 30iterations 0.2516749 9.404694 at 40iterations 0.1058461 3.559666 at 50iterations 4.4492051E-02 1.692257 at 60iterations 1.8666035E-02 0.7125244 at 70iterations 7.8559062E-03 0.2748604 at 80iterations 3.3124629E-03 0.1143570 at 90iterations 1.3921090E-03 5.3668976E-02 at 100iterations 5.8845192E-04 2.2077560E-02 at 110iterations 2.4771664E-04 8.2845688E-03 at 120iterations finished qdiffx linear iterations at : 17:03:48 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 2.4771664E-04 8.2845688E-03 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 17:03:48 8.156u 0.230s 0:08.99 93.2% 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 17:03:48 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 = 2966 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: 2.477268 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): -34.44700 30.22100 ymin,ymax (A): -21.20900 25.66200 zmin,zma (A): -40.26100 6.759000 x,y,z range (A): 64.66800 46.87100 47.02000 scale (grids/A): 2.477268 object centre (A): -2.113002 2.226500 -16.75100 number of atom coordinates read : 2966 total number of charged atoms : 2825 net assigned charge : -3.499968 assigned positive charge : 442.6930 centred at (gu) : 88.13532 90.99805 93.02546 assigned negative charge : -446.1941 centred at (gu) : 87.87475 90.34088 93.33686 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 149763 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26829 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 65378 mr = 105507 m= 17221 mr = 50619 m= 2615 mr = 12433 m= 154 mr = 1612 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 543 time to turn everything in is 1.210000 number of dielectric boundary points 64902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 22584 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) : 1.651512 object centre at (A) : -2.113002 2.226500 -16.75100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4167424E-02 -4.8714861E-02 midg,1,midg; midg,igrid,midg -0.2189090 0.1507621 1,midg,midg; igrid,midg,midg -0.6002463 0.2019843 gauss-seidel spectral radius is 0.9991547 estimated iterations to convergence 272 setup time was (sec) 1.560000 now iterating at: 17:03:50 rms-change max change #iterations 8.805598 356.9002 at 10iterations 4.951564 126.5996 at 20iterations 2.774253 72.41553 at 30iterations 1.547663 38.54203 at 40iterations 0.8577064 20.01192 at 50iterations 0.4787921 11.04661 at 60iterations 0.2652262 5.624698 at 70iterations 0.1471862 3.010872 at 80iterations 8.1249647E-02 1.859394 at 90iterations 4.5045111E-02 0.9234009 at 100iterations 2.4861312E-02 0.5778923 at 110iterations 1.3751508E-02 0.2792923 at 120iterations 7.5833220E-03 0.1705638 at 130iterations 4.1883253E-03 8.5119247E-02 at 140iterations 2.3194312E-03 5.3500175E-02 at 150iterations 1.2761774E-03 2.6730537E-02 at 160iterations 7.0539315E-04 1.6011238E-02 at 170iterations 3.8955678E-04 7.6980591E-03 at 180iterations finished qdiffx linear iterations at : 17:04:02 total time elapsed so far: 13.12000 # loops : 180 mean,max change (kT/e) : 3.8955678E-04 7.6980591E-03 energy calculations done at 13.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 17:04:03 13.314u 0.219s 0:14.27 94.7% 0+0k 0+0io 0pf+0w