Tue Oct 11 04:30:51 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 Tue Oct 11 2011 at 04:30:51 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2721 !!! WARNING: HIR 71 has a net charge of 0.5140 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: 0.6415686 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): -11.94100 37.04400 ymin,ymax (A): -25.92900 22.39700 zmin,zma (A): -10.08300 45.40600 x,y,z range (A): 48.98500 48.32600 55.48900 scale (grids/A): 0.6415686 object centre (A): 12.55150 -1.766000 17.66150 number of atom coordinates read : 2721 total number of charged atoms : 2573 net assigned charge : 3.514014 assigned positive charge : 415.8347 centred at (gu) : 90.22105 90.39616 91.88107 assigned negative charge : -412.3213 centred at (gu) : 89.96291 90.19961 91.83768 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7356 nv = 96 ne = 84 npr = 56173 no. pairs analyzed = 56173 no. exposed pairs = 3247 no. arc points = 22706 no. surface atoms = 1105 nbur = 1616 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 379 mr = 4133 m= 0 mr = 37 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2282 ## 234 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8955 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7130778E-10 1.5953686E-08 midg,1,midg; midg,igrid,midg -1.9048601E-08 3.2562067E-08 1,midg,midg; igrid,midg,midg -2.7747939E-08 3.9279954E-08 gauss-seidel spectral radius is 0.9874187 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 04:30:52 rms-change max change #iterations 0.1552675 21.94795 at 10iterations 1.5777320E-02 2.051353 at 20iterations 1.5731623E-03 0.2169895 at 30iterations 1.6020426E-04 2.3437500E-02 at 40iterations 1.6754486E-05 2.6931763E-03 at 50iterations finished qdiffx linear iterations at : 04:30:55 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.6754486E-05 2.6931763E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 04:30:56 3.406u 0.179s 0:04.11 86.8% 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 Tue Oct 11 2011 at 04:30:56 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2721 !!! WARNING: HIR 71 has a net charge of 0.5140 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: 1.924706 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): -11.94100 37.04400 ymin,ymax (A): -25.92900 22.39700 zmin,zma (A): -10.08300 45.40600 x,y,z range (A): 48.98500 48.32600 55.48900 scale (grids/A): 1.924706 object centre (A): 12.55150 -1.766000 17.66150 number of atom coordinates read : 2721 total number of charged atoms : 2573 net assigned charge : 3.514014 assigned positive charge : 415.8347 centred at (gu) : 90.66245 91.18767 95.64260 assigned negative charge : -412.3213 centred at (gu) : 89.88818 90.59846 95.51272 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 79797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22706 grid for indexing accessible points = 1.400000 m= 28947 mr = 56278 m= 4249 mr = 21463 m= 209 mr = 2609 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 857 time to turn everything in is 0.4000000 number of dielectric boundary points 32806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20249 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) : 0.6415686 object centre at (A) : 12.55150 -1.766000 17.66150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5356894E-02 1.1681910E-02 midg,1,midg; midg,igrid,midg -1.6281400E-02 3.0095842E-02 1,midg,midg; igrid,midg,midg -1.2384195E-02 5.5685189E-02 gauss-seidel spectral radius is 0.9986708 estimated iterations to convergence 217 setup time was (sec) 0.6200000 now iterating at: 04:30:56 rms-change max change #iterations 4.480430 171.3089 at 10iterations 2.117939 68.49422 at 20iterations 1.004207 31.63143 at 30iterations 0.4774982 14.23586 at 40iterations 0.2258848 6.363258 at 50iterations 0.1067996 3.231422 at 60iterations 5.0815057E-02 1.575336 at 70iterations 2.4096746E-02 0.7276754 at 80iterations 1.1385129E-02 0.3452988 at 90iterations 5.4089930E-03 0.1549482 at 100iterations 2.5664240E-03 7.6711655E-02 at 110iterations 1.2111221E-03 3.9840698E-02 at 120iterations finished qdiffx linear iterations at : 04:31:04 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.2111221E-03 3.9840698E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 04:31:04 7.868u 0.192s 0:08.43 95.4% 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 04:31:04 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2721 !!! WARNING: HIR 71 has a net charge of 0.5140 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: 2.887058 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): -11.94100 37.04400 ymin,ymax (A): -25.92900 22.39700 zmin,zma (A): -10.08300 45.40600 x,y,z range (A): 48.98500 48.32600 55.48900 scale (grids/A): 2.887058 object centre (A): 12.55150 -1.766000 17.66150 number of atom coordinates read : 2721 total number of charged atoms : 2573 net assigned charge : 3.514014 assigned positive charge : 415.8347 centred at (gu) : 90.99383 91.78149 98.46375 assigned negative charge : -412.3213 centred at (gu) : 89.83241 90.89767 98.26907 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 184516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22706 grid for indexing accessible points = 1.400000 m= 94728 mr = 136148 m= 33369 mr = 77981 m= 7485 mr = 26870 m= 935 mr = 5573 m= 53 mr = 568 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 2746 time to turn everything in is 1.020000 number of dielectric boundary points 73930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 20584 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) : 1.924706 object centre at (A) : 12.55150 -1.766000 17.66150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5132093 0.3681171 midg,1,midg; midg,igrid,midg -0.1798398 0.3233793 1,midg,midg; igrid,midg,midg -0.1261172 0.4488003 gauss-seidel spectral radius is 0.9992645 estimated iterations to convergence 291 setup time was (sec) 1.260000 now iterating at: 04:31:05 rms-change max change #iterations 10.55122 355.0142 at 10iterations 6.174319 134.1567 at 20iterations 3.602458 67.76261 at 30iterations 2.100339 42.48041 at 40iterations 1.217949 23.03070 at 50iterations 0.7062664 12.18351 at 60iterations 0.4084540 7.990425 at 70iterations 0.2359883 4.117543 at 80iterations 0.1366951 2.511489 at 90iterations 7.8699201E-02 1.290489 at 100iterations 4.5417294E-02 0.8741875 at 110iterations 2.6190782E-02 0.4650898 at 120iterations 1.5128154E-02 0.2597504 at 130iterations 8.7514259E-03 0.1522083 at 140iterations 5.0481264E-03 9.0110779E-02 at 150iterations 2.9142695E-03 5.4323196E-02 at 160iterations 1.6885705E-03 2.9884338E-02 at 170iterations 9.7997207E-04 1.7303467E-02 at 180iterations finished qdiffx linear iterations at : 04:31:17 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 9.7997207E-04 1.7303467E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 04:31:18 12.748u 0.209s 0:13.83 93.5% 0+0k 0+0io 0pf+0w