Sat Oct 8 11:35:58 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 11:35:58 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6209555 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): -60.81500 -14.21300 ymin,ymax (A): -75.70500 -23.57800 zmin,zma (A): -32.56500 24.76600 x,y,z range (A): 46.60200 52.12700 57.33100 scale (grids/A): 0.6209555 object centre (A): -37.51400 -49.64150 -3.899501 number of atom coordinates read : 2581 total number of charged atoms : 2421 net assigned charge : -0.9999937 assigned positive charge : 378.9127 centred at (gu) : 89.89784 92.19969 91.33143 assigned negative charge : -379.9134 centred at (gu) : 89.84498 92.15945 91.25878 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6720 nv = 96 ne = 84 npr = 52636 no. pairs analyzed = 52636 no. exposed pairs = 3335 no. arc points = 23194 no. surface atoms = 1130 nbur = 1451 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3558 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2295 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8083 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3368238E-09 5.1956714E-09 midg,1,midg; midg,igrid,midg -2.2495383E-09 2.8496259E-09 1,midg,midg; igrid,midg,midg -4.5892801E-09 2.4784710E-09 gauss-seidel spectral radius is 0.9865716 estimated iterations to convergence 71 setup time was (sec) 0.6100000 now iterating at: 11:35:59 rms-change max change #iterations 0.1266891 20.06346 at 10iterations 1.1549739E-02 1.699656 at 20iterations 1.0722262E-03 0.1508965 at 30iterations 1.0910443E-04 1.7406464E-02 at 40iterations 1.4188678E-05 2.2487640E-03 at 50iterations finished qdiffx linear iterations at : 11:36:03 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 1.4188678E-05 2.2487640E-03 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 11:36:03 4.510u 0.393s 0:05.25 93.3% 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 11:36:03 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.862867 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): -60.81500 -14.21300 ymin,ymax (A): -75.70500 -23.57800 zmin,zma (A): -32.56500 24.76600 x,y,z range (A): 46.60200 52.12700 57.33100 scale (grids/A): 1.862867 object centre (A): -37.51400 -49.64150 -3.899501 number of atom coordinates read : 2581 total number of charged atoms : 2421 net assigned charge : -0.9999937 assigned positive charge : 378.9127 centred at (gu) : 89.69315 96.59824 93.99361 assigned negative charge : -379.9134 centred at (gu) : 89.53452 96.47811 93.77625 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23194 grid for indexing accessible points = 1.400000 m= 25090 mr = 49398 m= 3391 mr = 17919 m= 132 mr = 1923 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 31817 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19000 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) : 0.6209555 object centre at (A) : -37.51400 -49.64150 -3.899501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4267083E-02 4.7132991E-02 midg,1,midg; midg,igrid,midg -9.9954447E-03 9.8498929E-03 1,midg,midg; igrid,midg,midg -5.5514416E-03 -8.4322514E-03 gauss-seidel spectral radius is 0.9985703 estimated iterations to convergence 210 setup time was (sec) 0.8900000 now iterating at: 11:36:05 rms-change max change #iterations 4.019776 179.6762 at 10iterations 1.845513 63.00266 at 20iterations 0.8493843 28.79219 at 30iterations 0.3907528 13.62069 at 40iterations 0.1795426 5.718792 at 50iterations 8.2611360E-02 2.731038 at 60iterations 3.7949551E-02 1.220802 at 70iterations 1.7460354E-02 0.6156497 at 80iterations 8.0441562E-03 0.2500838 at 90iterations 3.7107733E-03 0.1182861 at 100iterations 1.7051697E-03 5.7916641E-02 at 110iterations 7.8561326E-04 2.5595665E-02 at 120iterations finished qdiffx linear iterations at : 11:36:15 total time elapsed so far: 10.64000 # loops : 120 mean,max change (kT/e) : 7.8561326E-04 2.5595665E-02 energy calculations done at 10.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.80000 DelPhi exited at 11:36:15 10.804u 0.461s 0:11.60 97.0% 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 11:36:15 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.794300 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): -60.81500 -14.21300 ymin,ymax (A): -75.70500 -23.57800 zmin,zma (A): -32.56500 24.76600 x,y,z range (A): 46.60200 52.12700 57.33100 scale (grids/A): 2.794300 object centre (A): -37.51400 -49.64150 -3.899501 number of atom coordinates read : 2581 total number of charged atoms : 2421 net assigned charge : -0.9999937 assigned positive charge : 378.9127 centred at (gu) : 89.53953 99.89730 95.99034 assigned negative charge : -379.9134 centred at (gu) : 89.30167 99.71707 95.66430 start vw surface at 0.1200000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 167735 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23194 grid for indexing accessible points = 1.400000 m= 82236 mr = 120174 m= 28064 mr = 66242 m= 5918 mr = 21998 m= 689 mr = 4181 m= 38 mr = 378 m= 0 mr = 19 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.520000 number of dielectric boundary points 71688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 19368 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) : 1.862867 object centre at (A) : -37.51400 -49.64150 -3.899501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2249592 0.9340949 midg,1,midg; midg,igrid,midg -6.6511840E-02 0.2126293 1,midg,midg; igrid,midg,midg -2.9427473E-02 -0.1174579 gauss-seidel spectral radius is 0.9992454 estimated iterations to convergence 287 setup time was (sec) 1.830000 now iterating at: 11:36:17 rms-change max change #iterations 9.620816 324.4258 at 10iterations 5.627150 138.7543 at 20iterations 3.261541 65.30828 at 30iterations 1.886036 36.67271 at 40iterations 1.087613 22.50690 at 50iterations 0.6245602 13.21318 at 60iterations 0.3584920 6.980253 at 70iterations 0.2058873 4.157372 at 80iterations 0.1181656 2.534821 at 90iterations 6.7519061E-02 1.328259 at 100iterations 3.8739201E-02 0.7307129 at 110iterations 2.2183144E-02 0.4392186 at 120iterations 1.2673626E-02 0.2820895 at 130iterations 7.2711729E-03 0.1380005 at 140iterations 4.1610142E-03 7.9982281E-02 at 150iterations 2.3881851E-03 4.4996262E-02 at 160iterations 1.3751519E-03 2.4900436E-02 at 170iterations 7.9378928E-04 1.4831379E-02 at 180iterations finished qdiffx linear iterations at : 11:36:34 total time elapsed so far: 18.25000 # loops : 180 mean,max change (kT/e) : 7.9378928E-04 1.4831379E-02 energy calculations done at 18.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.42000 DelPhi exited at 11:36:35 18.427u 0.484s 0:19.56 96.6% 0+0k 0+0io 0pf+0w