Sun Oct 9 14:17:13 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 14:17:13 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2646 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 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: 0.5549234 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): -2.813000 49.22800 ymin,ymax (A): -8.663000 38.79800 zmin,zma (A): -16.15000 48.00300 x,y,z range (A): 52.04100 47.46100 64.15300 scale (grids/A): 0.5549234 object centre (A): 23.20750 15.06750 15.92650 number of atom coordinates read : 2646 total number of charged atoms : 2501 net assigned charge : 3.945009 assigned positive charge : 403.5957 centred at (gu) : 90.57835 90.56617 88.80963 assigned negative charge : -399.6514 centred at (gu) : 90.43142 90.42842 88.90829 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5324 nv = 96 ne = 84 npr = 52472 no. pairs analyzed = 52472 no. exposed pairs = 3414 no. arc points = 23601 no. surface atoms = 1153 nbur = 1493 mkacc time = 8.9999996E-02 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 = 1.540000 m= 208 mr = 2714 m= 1 mr = 13 m= 0 mr = 0 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 2806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2428 ## 289 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6856 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5154931E-09 -3.7374048E-10 midg,1,midg; midg,igrid,midg -7.2806716E-10 1.6612876E-09 1,midg,midg; igrid,midg,midg -7.9416612E-10 1.7511262E-09 gauss-seidel spectral radius is 0.9832258 estimated iterations to convergence 64 setup time was (sec) 0.4000000 now iterating at: 14:17:14 rms-change max change #iterations 7.8793027E-02 15.20361 at 10iterations 5.4164524E-03 1.013688 at 20iterations 3.8016847E-04 6.9832325E-02 at 30iterations 3.9848877E-05 9.7522736E-03 at 40iterations 9.4348188E-06 2.7446747E-03 at 50iterations finished qdiffx linear iterations at : 14:17:17 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 9.4348188E-06 2.7446747E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 14:17:18 3.704u 0.204s 0:04.22 92.4% 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 Sun Oct 9 2011 at 14:17:18 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2646 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 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: 1.664770 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): -2.813000 49.22800 ymin,ymax (A): -8.663000 38.79800 zmin,zma (A): -16.15000 48.00300 x,y,z range (A): 52.04100 47.46100 64.15300 scale (grids/A): 1.664770 object centre (A): 23.20750 15.06750 15.92650 number of atom coordinates read : 2646 total number of charged atoms : 2501 net assigned charge : 3.945009 assigned positive charge : 403.5957 centred at (gu) : 91.73434 91.69765 86.42825 assigned negative charge : -399.6514 centred at (gu) : 91.29390 91.28506 86.72451 start vw surface at 0.1000000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 58599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23601 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18412 mr = 39461 m= 1841 mr = 12491 m= 43 mr = 860 m= 0 mr = 4 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 26079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 309 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 19232 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) : 0.5549234 object centre at (A) : 23.20750 15.06750 15.92650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6230275E-02 5.1653883E-03 midg,1,midg; midg,igrid,midg -2.8031145E-03 5.0585694E-03 1,midg,midg; igrid,midg,midg -2.1692596E-02 -2.0206608E-03 gauss-seidel spectral radius is 0.9982232 estimated iterations to convergence 188 setup time was (sec) 0.5300000 now iterating at: 14:17:18 rms-change max change #iterations 3.234254 154.9070 at 10iterations 1.362109 49.28422 at 20iterations 0.5705159 25.04183 at 30iterations 0.2407272 9.055281 at 40iterations 0.1015917 3.763885 at 50iterations 4.2688459E-02 1.754391 at 60iterations 1.7939245E-02 0.6888170 at 70iterations 7.5759343E-03 0.3234596 at 80iterations 3.1966714E-03 0.1186562 at 90iterations 1.3535068E-03 6.0071945E-02 at 100iterations 5.7275221E-04 1.9858837E-02 at 110iterations 2.4390606E-04 9.2129707E-03 at 120iterations finished qdiffx linear iterations at : 14:17:25 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 2.4390606E-04 9.2129707E-03 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 14:17:26 7.774u 0.202s 0:08.46 94.2% 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 Sun Oct 9 2011 at 14:17:26 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2646 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 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: 2.497155 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): -2.813000 49.22800 ymin,ymax (A): -8.663000 38.79800 zmin,zma (A): -16.15000 48.00300 x,y,z range (A): 52.04100 47.46100 64.15300 scale (grids/A): 2.497155 object centre (A): 23.20750 15.06750 15.92650 number of atom coordinates read : 2646 total number of charged atoms : 2501 net assigned charge : 3.945009 assigned positive charge : 403.5957 centred at (gu) : 92.60132 92.54655 84.64236 assigned negative charge : -399.6514 centred at (gu) : 91.94077 91.92742 85.08664 start vw surface at 0.1000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 136076 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23601 grid for indexing accessible points = 1.400000 m= 63531 mr = 96722 m= 17760 mr = 49822 m= 2776 mr = 13090 m= 209 mr = 1825 m= 3 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 58819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 19986 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) : 1.664770 object centre at (A) : 23.20750 15.06750 15.92650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7153987 9.8785758E-02 midg,1,midg; midg,igrid,midg -3.9514139E-02 1.3576215E-02 1,midg,midg; igrid,midg,midg -0.3575353 -5.1919367E-02 gauss-seidel spectral radius is 0.9991409 estimated iterations to convergence 269 setup time was (sec) 0.9800000 now iterating at: 14:17:27 rms-change max change #iterations 8.465242 291.0324 at 10iterations 4.834146 125.6087 at 20iterations 2.730728 72.00152 at 30iterations 1.533231 40.15785 at 40iterations 0.8550785 22.60298 at 50iterations 0.4766476 11.26353 at 60iterations 0.2657719 5.921829 at 70iterations 0.1476776 3.347351 at 80iterations 8.1661776E-02 1.774073 at 90iterations 4.5079026E-02 0.9734559 at 100iterations 2.4905531E-02 0.5567236 at 110iterations 1.3751940E-02 0.3126125 at 120iterations 7.6133241E-03 0.1725769 at 130iterations 4.2001368E-03 9.9231720E-02 at 140iterations 2.3275649E-03 5.1368713E-02 at 150iterations 1.2890953E-03 2.9659271E-02 at 160iterations 7.1618875E-04 1.5438080E-02 at 170iterations 4.0166895E-04 1.0159492E-02 at 180iterations finished qdiffx linear iterations at : 14:17:39 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 4.0166895E-04 1.0159492E-02 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 14:17:39 12.296u 0.237s 0:12.87 97.2% 0+0k 0+0io 0pf+0w