Wed Dec 21 14:20:56 PST 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 Wed Dec 21 2011 at 14:20:56 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6410372 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): -3.919000 35.29600 ymin,ymax (A): -4.302000 48.73500 zmin,zma (A): -24.13700 31.39800 x,y,z range (A): 39.21500 53.03700 55.53500 scale (grids/A): 0.6410372 object centre (A): 15.68850 22.21650 3.630500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 287.8261 centred at (gu) : 90.11593 92.82070 90.00753 assigned negative charge : -283.8263 centred at (gu) : 90.17662 92.92558 89.94158 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5581 nv = 96 ne = 84 npr = 40147 no. pairs analyzed = 40147 no. exposed pairs = 2393 no. arc points = 16979 no. surface atoms = 818 nbur = 1144 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 274 mr = 3161 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.1700000 number of dielectric boundary points 2663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1692 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6493 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7915610E-10 1.1960081E-08 midg,1,midg; midg,igrid,midg 8.4489962E-09 -5.9312626E-09 1,midg,midg; igrid,midg,midg 1.1211998E-08 9.5818609E-10 gauss-seidel spectral radius is 0.9873359 estimated iterations to convergence 73 setup time was (sec) 0.4100000 now iterating at: 14:20:57 rms-change max change #iterations 0.1218505 18.43215 at 10iterations 1.2112415E-02 1.763332 at 20iterations 1.2208748E-03 0.2173176 at 30iterations 1.2041657E-04 2.0210266E-02 at 40iterations 1.1973429E-05 1.8253326E-03 at 50iterations finished qdiffx linear iterations at : 14:21:00 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 1.1973429E-05 1.8253326E-03 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 14:21:01 4.181u 0.289s 0:05.07 87.9% 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 Wed Dec 21 2011 at 14:21:01 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.923112 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): -3.919000 35.29600 ymin,ymax (A): -4.302000 48.73500 zmin,zma (A): -24.13700 31.39800 x,y,z range (A): 39.21500 53.03700 55.53500 scale (grids/A): 1.923112 object centre (A): 15.68850 22.21650 3.630500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 287.8261 centred at (gu) : 90.34788 98.46178 90.02258 assigned negative charge : -283.8263 centred at (gu) : 90.52996 98.77706 89.82490 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 59865 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16979 grid for indexing accessible points = 1.400000 m= 22642 mr = 41844 m= 3363 mr = 17484 m= 156 mr = 2188 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 2342 time to turn everything in is 0.3300000 number of dielectric boundary points 24466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14431 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) : 0.6410372 object centre at (A) : 15.68850 22.21650 3.630500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7195058E-02 2.3555003E-02 midg,1,midg; midg,igrid,midg 3.4585897E-02 6.8603735E-04 1,midg,midg; igrid,midg,midg 3.6933618E-03 -1.3591781E-03 gauss-seidel spectral radius is 0.9985815 estimated iterations to convergence 210 setup time was (sec) 0.5700000 now iterating at: 14:21:02 rms-change max change #iterations 3.593547 171.1531 at 10iterations 1.660508 64.68829 at 20iterations 0.7671097 27.10076 at 30iterations 0.3543879 12.29401 at 40iterations 0.1630442 5.877295 at 50iterations 7.5315826E-02 2.471381 at 60iterations 3.4805145E-02 1.164832 at 70iterations 1.6074404E-02 0.5917206 at 80iterations 7.3879543E-03 0.3035717 at 90iterations 3.4234750E-03 0.1139994 at 100iterations 1.5784595E-03 5.3255081E-02 at 110iterations 7.2792120E-04 2.5952816E-02 at 120iterations finished qdiffx linear iterations at : 14:21:12 total time elapsed so far: 10.44000 # loops : 120 mean,max change (kT/e) : 7.2792120E-04 2.5952816E-02 energy calculations done at 10.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.59000 DelPhi exited at 14:21:14 10.596u 0.433s 0:12.32 89.4% 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 Wed Dec 21 2011 at 14:21:14 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.884668 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): -3.919000 35.29600 ymin,ymax (A): -4.302000 48.73500 zmin,zma (A): -24.13700 31.39800 x,y,z range (A): 39.21500 53.03700 55.53500 scale (grids/A): 2.884668 object centre (A): 15.68850 22.21650 3.630500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 287.8261 centred at (gu) : 90.52185 102.6927 90.03396 assigned negative charge : -283.8263 centred at (gu) : 90.79499 103.1656 89.73741 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 138206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16979 grid for indexing accessible points = 1.400000 m= 72548 mr = 100936 m= 27124 mr = 60763 m= 6150 mr = 22748 m= 722 mr = 4680 m= 45 mr = 445 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 7888 time to turn everything in is 1.010000 number of dielectric boundary points 55204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 14640 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) : 1.923112 object centre at (A) : 15.68850 22.21650 3.630500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.114040 8.7769419E-02 midg,1,midg; midg,igrid,midg 0.3415196 -5.1696382E-02 1,midg,midg; igrid,midg,midg 1.9216623E-02 -6.3604885E-03 gauss-seidel spectral radius is 0.9992319 estimated iterations to convergence 285 setup time was (sec) 1.500000 now iterating at: 14:21:16 rms-change max change #iterations 8.474954 580.0781 at 10iterations 4.859638 114.1472 at 20iterations 2.766552 59.32467 at 30iterations 1.570153 35.41891 at 40iterations 0.8956515 18.80738 at 50iterations 0.5080463 11.08502 at 60iterations 0.2886440 6.334653 at 70iterations 0.1637765 3.436457 at 80iterations 9.3077682E-02 1.931816 at 90iterations 5.2775208E-02 1.071901 at 100iterations 2.9937254E-02 0.6322823 at 110iterations 1.6963132E-02 0.3620186 at 120iterations 9.6399998E-03 0.1877136 at 130iterations 5.4658088E-03 0.1085570 at 140iterations 3.0994914E-03 6.4489841E-02 at 150iterations 1.7602789E-03 3.7963152E-02 at 160iterations 9.9995371E-04 2.1440744E-02 at 170iterations 5.6823296E-04 1.1057854E-02 at 180iterations finished qdiffx linear iterations at : 14:21:28 total time elapsed so far: 13.75000 # loops : 180 mean,max change (kT/e) : 5.6823296E-04 1.1057854E-02 energy calculations done at 13.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.88000 DelPhi exited at 14:21:33 13.877u 0.597s 0:19.02 76.0% 0+0k 0+0io 0pf+0w