Mon Oct 10 16:57:37 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 Mon Oct 10 2011 at 16:57:37 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 = 2579 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5592824 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): -23.83500 26.27400 ymin,ymax (A): -19.69700 29.97900 zmin,zma (A): -8.271000 55.38200 x,y,z range (A): 50.10900 49.67600 63.65300 scale (grids/A): 0.5592824 object centre (A): 1.219501 5.141000 23.55550 number of atom coordinates read : 2579 total number of charged atoms : 2440 net assigned charge : 4.000016 assigned positive charge : 381.7670 centred at (gu) : 89.14540 91.07043 90.69034 assigned negative charge : -377.7678 centred at (gu) : 89.05370 91.00956 90.61501 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5295 nv = 96 ne = 84 npr = 51298 no. pairs analyzed = 51298 no. exposed pairs = 3432 no. arc points = 24520 no. surface atoms = 1151 nbur = 1428 mkacc time = 8.0000006E-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 = 1.540000 m= 213 mr = 2609 m= 4 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2402 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6771 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3882993E-10 1.2933705E-09 midg,1,midg; midg,igrid,midg -1.1260575E-10 1.2494648E-09 1,midg,midg; igrid,midg,midg -5.4818228E-10 1.0094704E-09 gauss-seidel spectral radius is 0.9834812 estimated iterations to convergence 64 setup time was (sec) 0.3900000 now iterating at: 16:57:38 rms-change max change #iterations 7.5472958E-02 13.15942 at 10iterations 5.4808250E-03 0.9984818 at 20iterations 4.9769174E-04 0.1031380 at 30iterations 8.0042279E-05 2.0092010E-02 at 40iterations 1.8171115E-05 4.7435760E-03 at 50iterations finished qdiffx linear iterations at : 16:57:41 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.8171115E-05 4.7435760E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 16:57:41 3.441u 0.167s 0:04.47 80.5% 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 Mon Oct 10 2011 at 16:57:42 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 = 2579 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.677847 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): -23.83500 26.27400 ymin,ymax (A): -19.69700 29.97900 zmin,zma (A): -8.271000 55.38200 x,y,z range (A): 50.10900 49.67600 63.65300 scale (grids/A): 1.677847 object centre (A): 1.219501 5.141000 23.55550 number of atom coordinates read : 2579 total number of charged atoms : 2440 net assigned charge : 4.000016 assigned positive charge : 381.7670 centred at (gu) : 87.43571 93.21058 92.07050 assigned negative charge : -377.7678 centred at (gu) : 87.16117 93.02831 91.84502 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 58074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24520 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18180 mr = 38293 m= 2037 mr = 12265 m= 54 mr = 945 m= 0 mr = 2 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 26840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 18772 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) : 0.5592824 object centre at (A) : 1.219501 5.141000 23.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9656455E-02 3.1406906E-02 midg,1,midg; midg,igrid,midg -1.9531853E-03 4.7668148E-04 1,midg,midg; igrid,midg,midg -9.1565000E-03 -1.5479153E-03 gauss-seidel spectral radius is 0.9982411 estimated iterations to convergence 189 setup time was (sec) 0.5100000 now iterating at: 16:57:42 rms-change max change #iterations 3.201254 176.8098 at 10iterations 1.342896 59.24956 at 20iterations 0.5681841 23.57577 at 30iterations 0.2408507 10.46193 at 40iterations 0.1016069 3.743644 at 50iterations 4.2949885E-02 1.691483 at 60iterations 1.8225254E-02 0.6979961 at 70iterations 7.7348719E-03 0.3137512 at 80iterations 3.2922730E-03 0.1165848 at 90iterations 1.4148725E-03 5.9152365E-02 at 100iterations 6.2018604E-04 2.3946762E-02 at 110iterations 2.8239482E-04 1.1595964E-02 at 120iterations finished qdiffx linear iterations at : 16:57:49 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 2.8239482E-04 1.1595964E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 16:57:50 7.739u 0.215s 0:08.72 91.0% 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 Mon Oct 10 2011 at 16:57:50 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 = 2579 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: 2.516771 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): -23.83500 26.27400 ymin,ymax (A): -19.69700 29.97900 zmin,zma (A): -8.271000 55.38200 x,y,z range (A): 50.10900 49.67600 63.65300 scale (grids/A): 2.516771 object centre (A): 1.219501 5.141000 23.55550 number of atom coordinates read : 2579 total number of charged atoms : 2440 net assigned charge : 4.000016 assigned positive charge : 381.7670 centred at (gu) : 86.15345 94.81591 93.10558 assigned negative charge : -377.7678 centred at (gu) : 85.74181 94.54250 92.76761 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 134945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24520 grid for indexing accessible points = 1.400000 m= 61880 mr = 94250 m= 18557 mr = 48212 m= 3135 mr = 13708 m= 240 mr = 1985 m= 4 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 60524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19505 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) : 1.677847 object centre at (A) : 1.219501 5.141000 23.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3452789 0.4003897 midg,1,midg; midg,igrid,midg -8.4880777E-03 -1.7804254E-03 1,midg,midg; igrid,midg,midg -9.2361115E-02 -2.9085588E-02 gauss-seidel spectral radius is 0.9991481 estimated iterations to convergence 271 setup time was (sec) 0.9500000 now iterating at: 16:57:52 rms-change max change #iterations 8.187854 334.5881 at 10iterations 4.614055 116.3809 at 20iterations 2.574118 68.96913 at 30iterations 1.436067 33.10769 at 40iterations 0.7973018 17.65687 at 50iterations 0.4419417 10.95196 at 60iterations 0.2441183 6.041779 at 70iterations 0.1348419 3.020351 at 80iterations 7.4427232E-02 1.742252 at 90iterations 4.1070342E-02 0.9202180 at 100iterations 2.2685096E-02 0.4703445 at 110iterations 1.2478662E-02 0.2645264 at 120iterations 6.8909586E-03 0.1527500 at 130iterations 3.7988094E-03 7.6360703E-02 at 140iterations 2.0966257E-03 4.7283173E-02 at 150iterations 1.1576471E-03 2.5183439E-02 at 160iterations 6.4298487E-04 1.4770508E-02 at 170iterations 3.5781565E-04 7.5883865E-03 at 180iterations finished qdiffx linear iterations at : 16:58:03 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 3.5781565E-04 7.5883865E-03 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.17000 DelPhi exited at 16:58:03 12.172u 0.219s 0:12.92 95.8% 0+0k 0+0io 0pf+0w