Mon Oct 10 14:03:19 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 Mon Oct 10 2011 at 14:03:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3109 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4949601 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): -12.22200 37.12000 ymin,ymax (A): -38.88100 25.01800 zmin,zma (A): -14.58000 57.34500 x,y,z range (A): 49.34200 63.89899 71.92500 scale (grids/A): 0.4949601 object centre (A): 12.44900 -6.931499 21.38250 number of atom coordinates read : 3109 total number of charged atoms : 2953 net assigned charge : 0.5000085 assigned positive charge : 461.2238 centred at (gu) : 89.93601 91.83231 88.85600 assigned negative charge : -460.7248 centred at (gu) : 89.95506 91.85458 88.83102 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 4958 nv = 96 ne = 84 npr = 59923 no. pairs analyzed = 59923 no. exposed pairs = 4286 no. arc points = 31235 no. surface atoms = 1452 nbur = 1657 mkacc time = 0.2000000 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 = 1.708000 m= 139 mr = 2218 m= 0 mr = 6 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 2873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3052 ## 543 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 6644 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3200131E-11 1.8211025E-11 midg,1,midg; midg,igrid,midg 1.3771517E-11 -2.4399378E-11 1,midg,midg; igrid,midg,midg 2.0275873E-11 -1.1647798E-11 gauss-seidel spectral radius is 0.9790313 estimated iterations to convergence 57 setup time was (sec) 0.7800000 now iterating at: 14:03:20 rms-change max change #iterations 4.3493781E-02 8.718475 at 10iterations 2.1646393E-03 0.4705830 at 20iterations 1.1597972E-04 1.9577026E-02 at 30iterations 8.0960244E-06 1.5792847E-03 at 40iterations 9.8330929E-07 2.1553040E-04 at 50iterations finished qdiffx linear iterations at : 14:03:24 total time elapsed so far: 4.670000 # loops : 50 mean,max change (kT/e) : 9.8330929E-07 2.1553040E-04 energy calculations done at 4.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.900000 DelPhi exited at 14:03:26 4.903u 0.393s 0:06.54 80.8% 0+0k 0+0io 6pf+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 14:03:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3109 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.484880 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): -12.22200 37.12000 ymin,ymax (A): -38.88100 25.01800 zmin,zma (A): -14.58000 57.34500 x,y,z range (A): 49.34200 63.89899 71.92500 scale (grids/A): 1.484880 object centre (A): 12.44900 -6.931499 21.38250 number of atom coordinates read : 3109 total number of charged atoms : 2953 net assigned charge : 0.5000085 assigned positive charge : 461.2238 centred at (gu) : 89.80730 95.49596 86.56716 assigned negative charge : -460.7248 centred at (gu) : 89.86469 95.56336 86.49249 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 55162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31235 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 13268 mr = 34182 m= 845 mr = 7948 m= 8 mr = 280 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 26873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 461 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 21877 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) : 0.4949601 object centre at (A) : 12.44900 -6.931499 21.38250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0867729E-03 7.6927379E-04 midg,1,midg; midg,igrid,midg 2.7321421E-03 1.2019006E-02 1,midg,midg; igrid,midg,midg -7.9794810E-04 -9.2519651E-04 gauss-seidel spectral radius is 0.9978175 estimated iterations to convergence 170 setup time was (sec) 0.9400000 now iterating at: 14:03:27 rms-change max change #iterations 2.680730 134.2535 at 10iterations 1.023198 50.33202 at 20iterations 0.3885779 18.53868 at 30iterations 0.1496678 6.416471 at 40iterations 5.7155151E-02 2.458539 at 50iterations 2.1703592E-02 0.8318882 at 60iterations 8.3111683E-03 0.3581142 at 70iterations 3.1790056E-03 0.1326797 at 80iterations 1.2194534E-03 5.6081057E-02 at 90iterations 4.6688912E-04 1.9260168E-02 at 100iterations 1.7834576E-04 7.2679520E-03 at 110iterations 6.8685971E-05 2.9602051E-03 at 120iterations finished qdiffx linear iterations at : 14:03:37 total time elapsed so far: 10.20000 # loops : 120 mean,max change (kT/e) : 6.8685971E-05 2.9602051E-03 energy calculations done at 10.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.40000 DelPhi exited at 14:03:38 10.405u 0.460s 0:12.40 87.5% 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 14:03:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3109 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.227320 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): -12.22200 37.12000 ymin,ymax (A): -38.88100 25.01800 zmin,zma (A): -14.58000 57.34500 x,y,z range (A): 49.34200 63.89899 71.92500 scale (grids/A): 2.227320 object centre (A): 12.44900 -6.931499 21.38250 number of atom coordinates read : 3109 total number of charged atoms : 2953 net assigned charge : 0.5000085 assigned positive charge : 461.2238 centred at (gu) : 89.71074 98.24381 84.85043 assigned negative charge : -460.7248 centred at (gu) : 89.79694 98.34470 84.73867 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 129021 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31235 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 49447 mr = 85387 m= 10148 mr = 36292 m= 1029 mr = 6719 m= 33 mr = 527 m= 0 mr = 5 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 60748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 23527 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) : 1.484880 object centre at (A) : 12.44900 -6.931499 21.38250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2143234 3.7615087E-02 midg,1,midg; midg,igrid,midg 3.4132034E-02 0.3543392 1,midg,midg; igrid,midg,midg -7.5985435E-03 -2.9039452E-02 gauss-seidel spectral radius is 0.9990260 estimated iterations to convergence 253 setup time was (sec) 1.720000 now iterating at: 14:03:41 rms-change max change #iterations 7.486227 234.3422 at 10iterations 4.066532 118.0044 at 20iterations 2.204890 60.42920 at 30iterations 1.180595 30.90516 at 40iterations 0.6312197 16.16312 at 50iterations 0.3357911 8.807037 at 60iterations 0.1784533 4.065811 at 70iterations 9.4944812E-02 2.441503 at 80iterations 5.0346788E-02 1.217155 at 90iterations 2.6665580E-02 0.6760502 at 100iterations 1.4130243E-02 0.3486724 at 110iterations 7.4793478E-03 0.1950235 at 120iterations 3.9552483E-03 9.5863342E-02 at 130iterations 2.0885924E-03 4.7429562E-02 at 140iterations 1.1060956E-03 2.5752068E-02 at 150iterations 5.8351044E-04 1.4476061E-02 at 160iterations 3.0835887E-04 7.4081421E-03 at 170iterations 1.6355161E-04 3.6191940E-03 at 180iterations finished qdiffx linear iterations at : 14:03:56 total time elapsed so far: 16.62000 # loops : 180 mean,max change (kT/e) : 1.6355161E-04 3.6191940E-03 energy calculations done at 16.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.85000 DelPhi exited at 14:03:56 16.857u 0.451s 0:17.66 97.9% 0+0k 0+0io 0pf+0w