Sat Oct 8 16:23:09 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 Sat Oct 8 2011 at 16:23:09 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 = 2372 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: 0.5868196 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): -2.266000 45.44000 ymin,ymax (A): -15.75800 29.62300 zmin,zma (A): -19.06100 41.60500 x,y,z range (A): 47.70600 45.38100 60.66600 scale (grids/A): 0.5868196 object centre (A): 21.58700 6.932500 11.27200 number of atom coordinates read : 2372 total number of charged atoms : 2288 net assigned charge : 4.000001 assigned positive charge : 352.0741 centred at (gu) : 90.45540 88.88143 88.86972 assigned negative charge : -348.0747 centred at (gu) : 90.49162 89.01177 88.89075 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5264 nv = 96 ne = 84 npr = 48731 no. pairs analyzed = 48731 no. exposed pairs = 2936 no. arc points = 20440 no. surface atoms = 1000 nbur = 1372 mkacc time = 7.9999998E-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 = 1.456000 m= 223 mr = 2790 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.1900000 number of dielectric boundary points 2683 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2065 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6810 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9669333E-09 4.8215965E-10 midg,1,midg; midg,igrid,midg 4.9732489E-09 -1.3575521E-09 1,midg,midg; igrid,midg,midg 1.6608175E-09 3.1079553E-10 gauss-seidel spectral radius is 0.9849555 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 16:23:10 rms-change max change #iterations 9.0900078E-02 15.84980 at 10iterations 7.4594324E-03 1.442679 at 20iterations 6.4466282E-04 0.1030579 at 30iterations 8.5614651E-05 1.6809940E-02 at 40iterations 1.9396035E-05 4.4324398E-03 at 50iterations finished qdiffx linear iterations at : 16:23:13 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 1.9396035E-05 4.4324398E-03 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 16:23:14 3.753u 0.233s 0:04.28 92.9% 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 16:23:14 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 = 2372 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: 1.760459 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): -2.266000 45.44000 ymin,ymax (A): -15.75800 29.62300 zmin,zma (A): -19.06100 41.60500 x,y,z range (A): 47.70600 45.38100 60.66600 scale (grids/A): 1.760459 object centre (A): 21.58700 6.932500 11.27200 number of atom coordinates read : 2372 total number of charged atoms : 2288 net assigned charge : 4.000001 assigned positive charge : 352.0741 centred at (gu) : 91.36578 86.64393 86.60863 assigned negative charge : -348.0747 centred at (gu) : 91.47479 87.03500 86.67223 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 58315 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20440 grid for indexing accessible points = 1.400000 m= 18618 mr = 39959 m= 2371 mr = 13202 m= 78 mr = 1376 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 842 time to turn everything in is 0.3000000 number of dielectric boundary points 24826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 226 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 17836 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) : 0.5868196 object centre at (A) : 21.58700 6.932500 11.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7623078E-02 1.5292574E-02 midg,1,midg; midg,igrid,midg 1.4679413E-02 -1.7844245E-03 1,midg,midg; igrid,midg,midg 2.9498788E-03 -1.7930135E-02 gauss-seidel spectral radius is 0.9983771 estimated iterations to convergence 197 setup time was (sec) 0.5300000 now iterating at: 16:23:14 rms-change max change #iterations 3.415944 172.5049 at 10iterations 1.500874 57.32634 at 20iterations 0.6538716 29.73289 at 30iterations 0.2879472 11.29249 at 40iterations 0.1265166 4.625063 at 50iterations 5.5104975E-02 1.979439 at 60iterations 2.4142772E-02 0.9846611 at 70iterations 1.0592188E-02 0.3681459 at 80iterations 4.6409396E-03 0.1667147 at 90iterations 2.0395764E-03 7.7372551E-02 at 100iterations 8.9327857E-04 3.1316936E-02 at 110iterations 3.9270261E-04 1.4529228E-02 at 120iterations finished qdiffx linear iterations at : 16:23:22 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 3.9270261E-04 1.4529228E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 16:23:22 8.020u 0.220s 0:08.54 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 Sat Oct 8 2011 at 16:23:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2372 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: 2.640688 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): -2.266000 45.44000 ymin,ymax (A): -15.75800 29.62300 zmin,zma (A): -19.06100 41.60500 x,y,z range (A): 47.70600 45.38100 60.66600 scale (grids/A): 2.640688 object centre (A): 21.58700 6.932500 11.27200 number of atom coordinates read : 2372 total number of charged atoms : 2288 net assigned charge : 4.000001 assigned positive charge : 352.0741 centred at (gu) : 92.04856 84.96576 84.91274 assigned negative charge : -348.0747 centred at (gu) : 92.21204 85.55237 85.00829 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 135459 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20440 grid for indexing accessible points = 1.400000 m= 62887 mr = 97771 m= 20026 mr = 50302 m= 3908 mr = 15604 m= 360 mr = 2900 m= 9 mr = 200 m= 0 mr = 3 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 2799 time to turn everything in is 0.7400000 number of dielectric boundary points 55869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 18299 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) : 1.760459 object centre at (A) : 21.58700 6.932500 11.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2151911 0.4837291 midg,1,midg; midg,igrid,midg 0.1596973 -3.1689785E-02 1,midg,midg; igrid,midg,midg 4.3100286E-02 -0.2866250 gauss-seidel spectral radius is 0.9991817 estimated iterations to convergence 276 setup time was (sec) 0.9900000 now iterating at: 16:23:23 rms-change max change #iterations 8.454318 314.7308 at 10iterations 4.826941 170.7782 at 20iterations 2.741933 86.51633 at 30iterations 1.548266 42.12957 at 40iterations 0.8739862 22.89917 at 50iterations 0.4926285 11.89526 at 60iterations 0.2768445 5.870191 at 70iterations 0.1550637 3.146312 at 80iterations 8.6884618E-02 2.059152 at 90iterations 4.8758917E-02 0.9880509 at 100iterations 2.7378125E-02 0.6067581 at 110iterations 1.5263525E-02 0.3437614 at 120iterations 8.5540731E-03 0.1779623 at 130iterations 4.7838022E-03 9.9010468E-02 at 140iterations 2.6702154E-03 5.4678440E-02 at 150iterations 1.4912403E-03 3.2794952E-02 at 160iterations 8.3465315E-04 1.7856598E-02 at 170iterations 4.6830982E-04 9.7064972E-03 at 180iterations finished qdiffx linear iterations at : 16:23:35 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 4.6830982E-04 9.7064972E-03 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 16:23:36 12.891u 0.243s 0:13.45 97.6% 0+0k 0+0io 0pf+0w