Mon Oct 10 22:43:17 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 Mon Oct 10 2011 at 22:43:17 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2618 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6264517 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): -19.86300 31.18200 ymin,ymax (A): 19.94800 76.77600 zmin,zma (A): 9.257999 51.92600 x,y,z range (A): 51.04500 56.82800 42.66800 scale (grids/A): 0.6264517 object centre (A): 5.659500 48.36200 30.59200 number of atom coordinates read : 2618 total number of charged atoms : 2477 net assigned charge : 4.500014 assigned positive charge : 393.8978 centred at (gu) : 91.43539 88.32677 89.79381 assigned negative charge : -389.3984 centred at (gu) : 91.40038 88.59946 89.98586 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6814 nv = 96 ne = 84 npr = 53519 no. pairs analyzed = 53519 no. exposed pairs = 3047 no. arc points = 21243 no. surface atoms = 1032 nbur = 1586 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3900 m= 0 mr = 28 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3000000 number of dielectric boundary points 3206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2039 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8293 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9850555E-08 -1.1209965E-08 midg,1,midg; midg,igrid,midg 3.6408121E-08 -1.2753684E-08 1,midg,midg; igrid,midg,midg 8.7724050E-10 9.1826760E-09 gauss-seidel spectral radius is 0.9868001 estimated iterations to convergence 71 setup time was (sec) 0.5400000 now iterating at: 22:43:18 rms-change max change #iterations 0.1413580 23.08794 at 10iterations 1.3544909E-02 2.423492 at 20iterations 1.6280316E-03 0.3333626 at 30iterations 3.6057556E-04 8.1939697E-02 at 40iterations 1.0091415E-04 2.4208069E-02 at 50iterations finished qdiffx linear iterations at : 22:43:22 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 1.0091415E-04 2.4208069E-02 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.380000 DelPhi exited at 22:43:22 4.382u 0.417s 0:05.20 92.1% 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 Mon Oct 10 2011 at 22:43:22 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2618 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.879355 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): -19.86300 31.18200 ymin,ymax (A): 19.94800 76.77600 zmin,zma (A): 9.257999 51.92600 x,y,z range (A): 51.04500 56.82800 42.66800 scale (grids/A): 1.879355 object centre (A): 5.659500 48.36200 30.59200 number of atom coordinates read : 2618 total number of charged atoms : 2477 net assigned charge : 4.500014 assigned positive charge : 393.8978 centred at (gu) : 94.30574 84.97956 89.38095 assigned negative charge : -389.3984 centred at (gu) : 94.20088 85.79812 89.95737 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 74091 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21243 grid for indexing accessible points = 1.400000 m= 25835 mr = 52595 m= 3969 mr = 19374 m= 200 mr = 2574 m= 1 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1455 time to turn everything in is 0.5900000 number of dielectric boundary points 29485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19449 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) : 0.6264517 object centre at (A) : 5.659500 48.36200 30.59200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3184666E-02 -1.2707799E-05 midg,1,midg; midg,igrid,midg 2.2272462E-02 -3.9497651E-02 1,midg,midg; igrid,midg,midg -9.7292557E-04 -3.1589705E-03 gauss-seidel spectral radius is 0.9985946 estimated iterations to convergence 211 setup time was (sec) 0.8800000 now iterating at: 22:43:24 rms-change max change #iterations 4.187950 181.7227 at 10iterations 1.929978 70.90863 at 20iterations 0.8930981 27.98384 at 30iterations 0.4126878 12.90110 at 40iterations 0.1920273 6.050747 at 50iterations 8.9404859E-02 2.819199 at 60iterations 4.1426830E-02 1.368843 at 70iterations 1.9302899E-02 0.6277313 at 80iterations 9.0441797E-03 0.2628937 at 90iterations 4.2850510E-03 0.1324692 at 100iterations 2.0804412E-03 7.2135925E-02 at 110iterations 1.0490094E-03 4.2476654E-02 at 120iterations finished qdiffx linear iterations at : 22:43:33 total time elapsed so far: 10.22000 # loops : 120 mean,max change (kT/e) : 1.0490094E-03 4.2476654E-02 energy calculations done at 10.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.39000 DelPhi exited at 22:43:34 10.392u 0.462s 0:11.25 96.4% 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 Mon Oct 10 2011 at 22:43:34 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2618 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.819033 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): -19.86300 31.18200 ymin,ymax (A): 19.94800 76.77600 zmin,zma (A): 9.257999 51.92600 x,y,z range (A): 51.04500 56.82800 42.66800 scale (grids/A): 2.819033 object centre (A): 5.659500 48.36200 30.59200 number of atom coordinates read : 2618 total number of charged atoms : 2477 net assigned charge : 4.500014 assigned positive charge : 393.8978 centred at (gu) : 96.45854 82.46933 89.07141 assigned negative charge : -389.3984 centred at (gu) : 96.30124 83.69717 89.93592 start vw surface at 0.1200000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 171719 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21243 grid for indexing accessible points = 1.400000 m= 85635 mr = 127243 m= 29918 mr = 71186 m= 7043 mr = 24310 m= 887 mr = 5438 m= 35 mr = 572 m= 0 mr = 15 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 5030 time to turn everything in is 1.540000 number of dielectric boundary points 66473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 19816 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) : 1.879355 object centre at (A) : 5.659500 48.36200 30.59200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3303043 4.1764829E-02 midg,1,midg; midg,igrid,midg -0.2190244 -0.3961339 1,midg,midg; igrid,midg,midg -8.1966527E-02 -8.7986410E-02 gauss-seidel spectral radius is 0.9992414 estimated iterations to convergence 287 setup time was (sec) 1.860000 now iterating at: 22:43:36 rms-change max change #iterations 9.706924 301.8989 at 10iterations 5.588614 138.3699 at 20iterations 3.205646 70.14091 at 30iterations 1.837012 34.43084 at 40iterations 1.051175 21.74117 at 50iterations 0.6011169 11.92123 at 60iterations 0.3434836 7.229406 at 70iterations 0.1964771 3.584825 at 80iterations 0.1123259 1.949227 at 90iterations 6.4143173E-02 1.308674 at 100iterations 3.6632523E-02 0.6891251 at 110iterations 2.0977978E-02 0.4012260 at 120iterations 1.2070647E-02 0.2256473 at 130iterations 6.9717509E-03 0.1275063 at 140iterations 4.0746354E-03 8.7158203E-02 at 150iterations 2.4296148E-03 4.9037933E-02 at 160iterations 1.5011283E-03 3.6983490E-02 at 170iterations 9.7236695E-04 2.3979187E-02 at 180iterations finished qdiffx linear iterations at : 22:43:53 total time elapsed so far: 19.04000 # loops : 180 mean,max change (kT/e) : 9.7236695E-04 2.3979187E-02 energy calculations done at 19.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.21000 DelPhi exited at 22:43:54 19.210u 0.474s 0:20.02 98.3% 0+0k 0+0io 0pf+0w