Sat Oct 8 12:49:39 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 12:49:39 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 = 2240 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: 0.6055863 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): -6.902000 51.88400 ymin,ymax (A): -14.95100 34.22400 zmin,zma (A): -14.43100 29.88000 x,y,z range (A): 58.78600 49.17500 44.31100 scale (grids/A): 0.6055863 object centre (A): 22.49100 9.636499 7.724500 number of atom coordinates read : 2240 total number of charged atoms : 2105 net assigned charge : -3.499987 assigned positive charge : 301.0929 centred at (gu) : 90.02491 88.72624 89.99649 assigned negative charge : -304.5934 centred at (gu) : 89.78086 88.80398 89.93532 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5753 nv = 96 ne = 84 npr = 46437 no. pairs analyzed = 46437 no. exposed pairs = 3027 no. arc points = 21393 no. surface atoms = 1034 nbur = 1206 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 289 mr = 2859 m= 0 mr = 27 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1973 ## 137 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6865 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9155217E-09 2.4244065E-10 midg,1,midg; midg,igrid,midg 1.1050234E-09 -3.3752674E-09 1,midg,midg; igrid,midg,midg -1.0286475E-08 6.2765309E-09 gauss-seidel spectral radius is 0.9858700 estimated iterations to convergence 69 setup time was (sec) 0.3800000 now iterating at: 12:49:40 rms-change max change #iterations 0.1001003 18.25898 at 10iterations 9.6379882E-03 1.700745 at 20iterations 1.7935734E-03 0.3707771 at 30iterations 6.0167524E-04 0.1341591 at 40iterations 2.1916110E-04 4.8732758E-02 at 50iterations finished qdiffx linear iterations at : 12:49:43 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 2.1916110E-04 4.8732758E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 12:49:43 3.502u 0.173s 0:03.99 91.9% 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 12:49:43 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 = 2240 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: 1.816759 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): -6.902000 51.88400 ymin,ymax (A): -14.95100 34.22400 zmin,zma (A): -14.43100 29.88000 x,y,z range (A): 58.78600 49.17500 44.31100 scale (grids/A): 1.816759 object centre (A): 22.49100 9.636499 7.724500 number of atom coordinates read : 2240 total number of charged atoms : 2105 net assigned charge : -3.499987 assigned positive charge : 301.0929 centred at (gu) : 90.07458 86.17867 89.98943 assigned negative charge : -304.5934 centred at (gu) : 89.34287 86.41212 89.80630 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 62752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21393 grid for indexing accessible points = 1.400000 m= 20372 mr = 41563 m= 2965 mr = 13692 m= 138 mr = 1555 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 29371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 16510 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) : 0.6055863 object centre at (A) : 22.49100 9.636499 7.724500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1139449E-03 -4.1754809E-03 midg,1,midg; midg,igrid,midg -1.3193646E-03 -4.7838907E-03 1,midg,midg; igrid,midg,midg -3.6601946E-02 2.4045182E-02 gauss-seidel spectral radius is 0.9984807 estimated iterations to convergence 203 setup time was (sec) 0.5400000 now iterating at: 12:49:44 rms-change max change #iterations 3.372657 189.9931 at 10iterations 1.506325 64.50107 at 20iterations 0.6761779 29.27950 at 30iterations 0.3025485 11.09372 at 40iterations 0.1364571 4.400783 at 50iterations 6.1428331E-02 2.158371 at 60iterations 2.7858984E-02 1.345108 at 70iterations 1.2854558E-02 0.4419653 at 80iterations 6.1181630E-03 0.2375965 at 90iterations 3.1345915E-03 0.1605110 at 100iterations 1.7565857E-03 7.7468872E-02 at 110iterations 1.0937876E-03 5.0415039E-02 at 120iterations finished qdiffx linear iterations at : 12:49:52 total time elapsed so far: 8.160000 # loops : 120 mean,max change (kT/e) : 1.0937876E-03 5.0415039E-02 energy calculations done at 8.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 12:49:52 8.292u 0.248s 0:08.83 96.6% 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 12:49:52 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 = 2240 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: 2.725138 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): -6.902000 51.88400 ymin,ymax (A): -14.95100 34.22400 zmin,zma (A): -14.43100 29.88000 x,y,z range (A): 58.78600 49.17500 44.31100 scale (grids/A): 2.725138 object centre (A): 22.49100 9.636499 7.724500 number of atom coordinates read : 2240 total number of charged atoms : 2105 net assigned charge : -3.499987 assigned positive charge : 301.0929 centred at (gu) : 90.11190 84.26809 89.98411 assigned negative charge : -304.5934 centred at (gu) : 89.01445 84.61822 89.70954 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 145455 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21393 grid for indexing accessible points = 1.400000 m= 67174 mr = 101869 m= 22698 mr = 52227 m= 5106 mr = 17007 m= 643 mr = 3420 m= 29 mr = 394 m= 0 mr = 11 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7900000 number of dielectric boundary points 66177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 16838 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) : 1.816759 object centre at (A) : 22.49100 9.636499 7.724500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5112193E-02 -3.0324696E-02 midg,1,midg; midg,igrid,midg -3.5861328E-02 -3.3539087E-02 1,midg,midg; igrid,midg,midg -0.5041942 0.4482041 gauss-seidel spectral radius is 0.9992152 estimated iterations to convergence 282 setup time was (sec) 1.030000 now iterating at: 12:49:54 rms-change max change #iterations 8.106830 323.9821 at 10iterations 4.684118 122.6091 at 20iterations 2.676987 64.56171 at 30iterations 1.529147 37.08447 at 40iterations 0.8681692 19.08352 at 50iterations 0.4924225 10.13343 at 60iterations 0.2802706 5.623823 at 70iterations 0.1587374 3.554275 at 80iterations 9.0020761E-02 1.807684 at 90iterations 5.0978906E-02 1.135967 at 100iterations 2.8824195E-02 0.6519482 at 110iterations 1.6377699E-02 0.3441181 at 120iterations 9.3005029E-03 0.1846104 at 130iterations 5.3254664E-03 0.1170731 at 140iterations 3.0944664E-03 6.4941406E-02 at 150iterations 1.8357929E-03 4.1755676E-02 at 160iterations 1.1460466E-03 3.0090332E-02 at 170iterations 7.5727567E-04 2.0088196E-02 at 180iterations finished qdiffx linear iterations at : 12:50:05 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 7.5727567E-04 2.0088196E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 12:50:06 12.917u 0.244s 0:13.46 97.6% 0+0k 0+0io 0pf+0w