Sat Oct 8 14:28:20 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 14:28:20 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6419388 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): -11.98600 43.47100 ymin,ymax (A): -23.77600 22.41900 zmin,zma (A): -7.933000 47.42800 x,y,z range (A): 55.45700 46.19500 55.36100 scale (grids/A): 0.6419388 object centre (A): 15.74250 -0.6785002 19.74750 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : 1.4008060E-02 assigned positive charge : 454.8726 centred at (gu) : 88.70206 90.01180 91.74993 assigned negative charge : -454.8593 centred at (gu) : 88.69131 89.92537 91.66498 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8156 nv = 96 ne = 84 npr = 64578 no. pairs analyzed = 64578 no. exposed pairs = 3444 no. arc points = 23327 no. surface atoms = 1169 nbur = 1860 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 448 mr = 4824 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3300000 number of dielectric boundary points 3730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2218 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9964 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5618108E-09 1.7466716E-08 midg,1,midg; midg,igrid,midg -1.2666884E-08 1.2124638E-08 1,midg,midg; igrid,midg,midg -2.3010769E-09 1.0228884E-09 gauss-seidel spectral radius is 0.9874547 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 14:28:21 rms-change max change #iterations 0.1682307 23.44997 at 10iterations 1.6719695E-02 1.987509 at 20iterations 1.7029191E-03 0.2249184 at 30iterations 1.8991131E-04 2.4089813E-02 at 40iterations 2.9390010E-05 3.8995743E-03 at 50iterations finished qdiffx linear iterations at : 14:28:23 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 2.9390010E-05 3.8995743E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 14:28:24 3.113u 0.159s 0:03.54 92.0% 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 14:28:24 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.925816 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): -11.98600 43.47100 ymin,ymax (A): -23.77600 22.41900 zmin,zma (A): -7.933000 47.42800 x,y,z range (A): 55.45700 46.19500 55.36100 scale (grids/A): 1.925816 object centre (A): 15.74250 -0.6785002 19.74750 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : 1.4008060E-02 assigned positive charge : 454.8726 centred at (gu) : 86.10531 90.03473 95.24895 assigned negative charge : -454.8593 centred at (gu) : 86.07339 89.77584 94.99475 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 89261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23327 grid for indexing accessible points = 1.400000 m= 32916 mr = 65090 m= 4980 mr = 24904 m= 282 mr = 3127 m= 7 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 547 time to turn everything in is 0.6000000 number of dielectric boundary points 34239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 22693 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) : 0.6419388 object centre at (A) : 15.74250 -0.6785002 19.74750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8179366E-02 2.1550754E-02 midg,1,midg; midg,igrid,midg 3.2408112E-03 2.3972023E-02 1,midg,midg; igrid,midg,midg -3.7625074E-02 6.1932504E-03 gauss-seidel spectral radius is 0.9986918 estimated iterations to convergence 219 setup time was (sec) 0.8700000 now iterating at: 14:28:25 rms-change max change #iterations 4.756913 193.9114 at 10iterations 2.279721 68.90120 at 20iterations 1.083907 33.80031 at 30iterations 0.5181604 13.85491 at 40iterations 0.2462226 7.342522 at 50iterations 0.1175723 3.176718 at 60iterations 5.6122731E-02 1.556499 at 70iterations 2.6766675E-02 0.8647308 at 80iterations 1.2757387E-02 0.4112530 at 90iterations 6.1100656E-03 0.1863174 at 100iterations 2.9083069E-03 8.9889526E-02 at 110iterations 1.3872640E-03 3.9592743E-02 at 120iterations finished qdiffx linear iterations at : 14:28:31 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 1.3872640E-03 3.9592743E-02 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 14:28:31 6.976u 0.171s 0:07.41 96.3% 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 8 2011 at 14:28:31 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.888725 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): -11.98600 43.47100 ymin,ymax (A): -23.77600 22.41900 zmin,zma (A): -7.933000 47.42800 x,y,z range (A): 55.45700 46.19500 55.36100 scale (grids/A): 2.888725 object centre (A): 15.74250 -0.6785002 19.74750 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : 1.4008060E-02 assigned positive charge : 454.8726 centred at (gu) : 84.15794 90.05205 97.87329 assigned negative charge : -454.8593 centred at (gu) : 84.11002 89.66376 97.49219 start vw surface at 0.1400000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 206923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23327 grid for indexing accessible points = 1.400000 m= 107229 mr = 157072 m= 38553 mr = 89812 m= 8931 mr = 31317 m= 1212 mr = 6601 m= 74 mr = 794 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1965 time to turn everything in is 1.500000 number of dielectric boundary points 77306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 23055 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) : 1.925816 object centre at (A) : 15.74250 -0.6785002 19.74750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1822418 0.2896837 midg,1,midg; midg,igrid,midg 5.0112262E-02 0.2925895 1,midg,midg; igrid,midg,midg -0.4513590 0.1589483 gauss-seidel spectral radius is 0.9992746 estimated iterations to convergence 293 setup time was (sec) 1.780000 now iterating at: 14:28:33 rms-change max change #iterations 11.00261 395.7828 at 10iterations 6.448915 142.7257 at 20iterations 3.759797 70.72544 at 30iterations 2.191165 39.24208 at 40iterations 1.274574 26.06696 at 50iterations 0.7411415 13.41446 at 60iterations 0.4302295 8.456530 at 70iterations 0.2496580 4.136175 at 80iterations 0.1445809 2.450327 at 90iterations 8.3871536E-02 1.439058 at 100iterations 4.8462704E-02 0.8582126 at 110iterations 2.8199920E-02 0.4890556 at 120iterations 1.6415022E-02 0.2624397 at 130iterations 9.5451949E-03 0.1811423 at 140iterations 5.5997269E-03 9.1987610E-02 at 150iterations 3.3129952E-03 5.7277679E-02 at 160iterations 1.9967470E-03 3.4584045E-02 at 170iterations 1.2382211E-03 2.2514343E-02 at 180iterations finished qdiffx linear iterations at : 14:28:43 total time elapsed so far: 11.21000 # loops : 180 mean,max change (kT/e) : 1.2382211E-03 2.2514343E-02 energy calculations done at 11.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.39000 DelPhi exited at 14:28:43 11.393u 0.172s 0:11.83 97.7% 0+0k 0+0io 0pf+0w