Sat Oct 15 14:13:50 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 14:13:50 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4674 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: ZN8 811 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5228681 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): -24.24200 40.39100 ymin,ymax (A): -18.12300 46.91000 zmin,zma (A): 7.018000 75.10400 x,y,z range (A): 64.63300 65.03300 68.08601 scale (grids/A): 0.5228681 object centre (A): 8.074502 14.39350 41.06100 number of atom coordinates read : 4674 total number of charged atoms : 4434 net assigned charge : 10.20003 assigned positive charge : 709.3415 centred at (gu) : 91.19839 88.56100 87.82703 assigned negative charge : -699.1456 centred at (gu) : 91.29932 88.69244 87.67328 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8192 nv = 96 ne = 84 npr = 92837 no. pairs analyzed = 92837 no. exposed pairs = 6152 no. arc points = 42575 no. surface atoms = 2058 nbur = 2616 mkacc time = 0.1600000 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 = 1.624000 m= 331 mr = 4187 m= 0 mr = 7 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4143 ## 598 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 10834 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2211465E-10 5.1090931E-10 midg,1,midg; midg,igrid,midg 1.1627103E-09 -2.0492620E-10 1,midg,midg; igrid,midg,midg 4.9715482E-10 -2.3837585E-10 gauss-seidel spectral radius is 0.9812885 estimated iterations to convergence 60 setup time was (sec) 0.5500000 now iterating at: 14:13:51 rms-change max change #iterations 7.5215347E-02 11.54437 at 10iterations 5.4723164E-03 0.7633228 at 20iterations 1.3889696E-03 0.2000513 at 30iterations 6.0523616E-04 8.6936951E-02 at 40iterations 2.7052886E-04 3.8596153E-02 at 50iterations finished qdiffx linear iterations at : 14:13:54 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 2.7052886E-04 3.8596153E-02 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 14:13:55 4.074u 0.249s 0:04.89 88.1% 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 14:13:55 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4674 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: ZN8 811 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.568604 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): -24.24200 40.39100 ymin,ymax (A): -18.12300 46.91000 zmin,zma (A): 7.018000 75.10400 x,y,z range (A): 64.63300 65.03300 68.08601 scale (grids/A): 1.568604 object centre (A): 8.074502 14.39350 41.06100 number of atom coordinates read : 4674 total number of charged atoms : 4434 net assigned charge : 10.20003 assigned positive charge : 709.3415 centred at (gu) : 93.59345 85.68178 83.48003 assigned negative charge : -699.1456 centred at (gu) : 93.89757 86.07726 83.01970 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 92490 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42575 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 27261 mr = 62861 m= 2536 mr = 18038 m= 57 mr = 1083 m= 0 mr = 6 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 133 time to turn everything in is 0.4700000 number of dielectric boundary points 40356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 482 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 33508 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) : 0.5228681 object centre at (A) : 8.074502 14.39350 41.06100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7712464E-03 2.3701614E-02 midg,1,midg; midg,igrid,midg 1.2971976E-02 -9.8370453E-03 1,midg,midg; igrid,midg,midg 1.5050936E-02 4.4174548E-03 gauss-seidel spectral radius is 0.9982051 estimated iterations to convergence 187 setup time was (sec) 0.7400000 now iterating at: 14:13:56 rms-change max change #iterations 3.982551 144.7337 at 10iterations 1.668999 54.34008 at 20iterations 0.6993223 22.81339 at 30iterations 0.2939234 8.947987 at 40iterations 0.1231705 3.852169 at 50iterations 5.2032694E-02 1.542027 at 60iterations 2.2032944E-02 0.7358971 at 70iterations 9.5965127E-03 0.3285646 at 80iterations 4.4484213E-03 0.1401291 at 90iterations 2.3239909E-03 8.6616516E-02 at 100iterations 1.4218895E-03 4.9053192E-02 at 110iterations 9.7959663E-04 3.4103394E-02 at 120iterations finished qdiffx linear iterations at : 14:14:04 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 9.7959663E-04 3.4103394E-02 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.330000 DelPhi exited at 14:14:05 9.335u 0.300s 0:10.10 95.3% 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 Sat Oct 15 2011 at 14:14:05 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4674 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: ZN8 811 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.352906 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): -24.24200 40.39100 ymin,ymax (A): -18.12300 46.91000 zmin,zma (A): 7.018000 75.10400 x,y,z range (A): 64.63300 65.03300 68.08601 scale (grids/A): 2.352906 object centre (A): 8.074502 14.39350 41.06100 number of atom coordinates read : 4674 total number of charged atoms : 4434 net assigned charge : 10.20003 assigned positive charge : 709.3415 centred at (gu) : 95.38977 83.52235 80.21970 assigned negative charge : -699.1456 centred at (gu) : 95.84631 84.11578 79.52941 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 215209 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42575 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 96753 mr = 154338 m= 25188 mr = 75246 m= 3700 mr = 17943 m= 215 mr = 2308 m= 5 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 394 time to turn everything in is 1.180000 number of dielectric boundary points 91153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 35400 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) : 1.568604 object centre at (A) : 8.074502 14.39350 41.06100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5788108 0.5264288 midg,1,midg; midg,igrid,midg 0.1574200 -0.1905742 1,midg,midg; igrid,midg,midg 0.2752918 9.5669836E-02 gauss-seidel spectral radius is 0.9991886 estimated iterations to convergence 277 setup time was (sec) 1.490000 now iterating at: 14:14:07 rms-change max change #iterations 10.59009 309.4336 at 10iterations 6.111250 183.3781 at 20iterations 3.507309 69.05167 at 30iterations 2.003613 45.35162 at 40iterations 1.136195 24.05513 at 50iterations 0.6437726 13.52577 at 60iterations 0.3644826 8.076548 at 70iterations 0.2055942 4.448315 at 80iterations 0.1160710 2.478739 at 90iterations 6.5246485E-02 1.279716 at 100iterations 3.6695521E-02 0.6753387 at 110iterations 2.0686872E-02 0.3859406 at 120iterations 1.1608028E-02 0.2130547 at 130iterations 6.5368097E-03 0.1225481 at 140iterations 3.6933096E-03 7.2011948E-02 at 150iterations 2.0949084E-03 4.1076660E-02 at 160iterations 1.2058835E-03 2.3343563E-02 at 170iterations 7.1130623E-04 1.8377304E-02 at 180iterations finished qdiffx linear iterations at : 14:14:28 total time elapsed so far: 15.86000 # loops : 180 mean,max change (kT/e) : 7.1130623E-04 1.8377304E-02 energy calculations done at 15.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.99000 DelPhi exited at 14:14:29 15.994u 0.317s 0:23.56 69.1% 0+0k 0+0io 0pf+0w