Sat Oct 8 18:44:31 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 Sat Oct 8 2011 at 18:44:31 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2574 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 459 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6267605 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): -32.06600 17.60300 ymin,ymax (A): -23.51100 23.14700 zmin,zma (A): -12.22100 44.57900 x,y,z range (A): 49.66900 46.65800 56.80000 scale (grids/A): 0.6267605 object centre (A): -7.231499 -0.1820002 16.17900 number of atom coordinates read : 2574 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 88.56358 89.13094 89.74706 assigned negative charge : -387.9385 centred at (gu) : 88.48737 89.17552 89.63139 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6663 nv = 96 ne = 84 npr = 52902 no. pairs analyzed = 52902 no. exposed pairs = 2962 no. arc points = 21358 no. surface atoms = 1003 nbur = 1571 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 366 mr = 3750 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.2000000 number of dielectric boundary points 3224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2144 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8166 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8080953E-09 1.2424654E-08 midg,1,midg; midg,igrid,midg 9.0774295E-09 3.1551892E-10 1,midg,midg; igrid,midg,midg -3.1787097E-09 7.3510473E-09 gauss-seidel spectral radius is 0.9868109 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 18:44:32 rms-change max change #iterations 0.1364109 18.95043 at 10iterations 1.2911829E-02 2.003845 at 20iterations 1.2196106E-03 0.1645813 at 30iterations 1.1812572E-04 1.6571045E-02 at 40iterations 1.1222014E-05 1.5869141E-03 at 50iterations finished qdiffx linear iterations at : 18:44:35 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 1.1222014E-05 1.5869141E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 18:44:35 3.620u 0.203s 0:04.10 93.1% 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 8 2011 at 18:44:35 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2574 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 459 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.880282 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): -32.06600 17.60300 ymin,ymax (A): -23.51100 23.14700 zmin,zma (A): -12.22100 44.57900 x,y,z range (A): 49.66900 46.65800 56.80000 scale (grids/A): 1.880282 object centre (A): -7.231499 -0.1820002 16.17900 number of atom coordinates read : 2574 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 85.69053 87.39252 89.24097 assigned negative charge : -387.9385 centred at (gu) : 85.46193 87.52620 88.89394 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21358 grid for indexing accessible points = 1.400000 m= 26516 mr = 51038 m= 4000 mr = 20014 m= 193 mr = 2587 m= 0 mr = 81 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1450 time to turn everything in is 0.3700000 number of dielectric boundary points 29679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19216 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) : 0.6267605 object centre at (A) : -7.231499 -0.1820002 16.17900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0005498E-02 2.2630259E-02 midg,1,midg; midg,igrid,midg 1.5353944E-02 2.2316708E-03 1,midg,midg; igrid,midg,midg -1.6287584E-03 2.8866781E-02 gauss-seidel spectral radius is 0.9985964 estimated iterations to convergence 212 setup time was (sec) 0.6000000 now iterating at: 18:44:36 rms-change max change #iterations 4.135241 159.7784 at 10iterations 1.919571 62.51160 at 20iterations 0.8928921 27.57403 at 30iterations 0.4116831 14.15442 at 40iterations 0.1914090 6.382954 at 50iterations 8.8756636E-02 3.049974 at 60iterations 4.1284584E-02 1.326142 at 70iterations 1.9156106E-02 0.6312103 at 80iterations 8.8755973E-03 0.3080673 at 90iterations 4.1076574E-03 0.1297789 at 100iterations 1.9058845E-03 6.2490463E-02 at 110iterations 8.8438345E-04 2.7282715E-02 at 120iterations finished qdiffx linear iterations at : 18:44:44 total time elapsed so far: 8.110000 # loops : 120 mean,max change (kT/e) : 8.8438345E-04 2.7282715E-02 energy calculations done at 8.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 18:44:44 8.246u 0.240s 0:08.75 96.9% 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 Sat Oct 8 2011 at 18:44:44 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2574 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 459 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.820422 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): -32.06600 17.60300 ymin,ymax (A): -23.51100 23.14700 zmin,zma (A): -12.22100 44.57900 x,y,z range (A): 49.66900 46.65800 56.80000 scale (grids/A): 2.820422 object centre (A): -7.231499 -0.1820002 16.17900 number of atom coordinates read : 2574 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 83.53558 86.08868 88.86129 assigned negative charge : -387.9385 centred at (gu) : 83.19283 86.28920 88.34084 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 167789 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21358 grid for indexing accessible points = 1.400000 m= 86004 mr = 123125 m= 31048 mr = 71418 m= 7192 mr = 25327 m= 949 mr = 5568 m= 39 mr = 676 m= 0 mr = 13 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 4773 time to turn everything in is 0.9400000 number of dielectric boundary points 66894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 19599 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) : 1.880282 object centre at (A) : -7.231499 -0.1820002 16.17900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4891707E-02 0.2902197 midg,1,midg; midg,igrid,midg 0.1793025 1.2426871E-02 1,midg,midg; igrid,midg,midg 4.1620787E-03 0.3710009 gauss-seidel spectral radius is 0.9992428 estimated iterations to convergence 287 setup time was (sec) 1.190000 now iterating at: 18:44:46 rms-change max change #iterations 9.633128 276.2268 at 10iterations 5.565433 127.7631 at 20iterations 3.189464 62.82391 at 30iterations 1.829483 37.16647 at 40iterations 1.046460 18.78683 at 50iterations 0.5978755 10.70860 at 60iterations 0.3418546 6.317717 at 70iterations 0.1956734 3.626687 at 80iterations 0.1117705 1.982748 at 90iterations 6.3819483E-02 1.138634 at 100iterations 3.6449347E-02 0.7055016 at 110iterations 2.0761635E-02 0.3743896 at 120iterations 1.1881949E-02 0.2332220 at 130iterations 6.8004774E-03 0.1287117 at 140iterations 3.8847937E-03 7.4249268E-02 at 150iterations 2.2234162E-03 4.1616440E-02 at 160iterations 1.2747705E-03 2.5444031E-02 at 170iterations 7.3191896E-04 1.3143063E-02 at 180iterations finished qdiffx linear iterations at : 18:44:58 total time elapsed so far: 13.16000 # loops : 180 mean,max change (kT/e) : 7.3191896E-04 1.3143063E-02 energy calculations done at 13.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.30000 DelPhi exited at 18:44:58 13.304u 0.226s 0:13.80 97.9% 0+0k 0+0io 0pf+0w