Mon Oct 10 17:04:45 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 Mon Oct 10 2011 at 17:04:45 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2572 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: 0.6134652 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): 9.707000 60.87700 ymin,ymax (A): 8.746000 57.35400 zmin,zma (A): 9.040000 67.07100 x,y,z range (A): 51.17000 48.60800 58.03100 scale (grids/A): 0.6134652 object centre (A): 35.29200 33.05000 38.05550 number of atom coordinates read : 2572 total number of charged atoms : 2406 net assigned charge : 4.500022 assigned positive charge : 377.3360 centred at (gu) : 90.63818 89.37272 89.23540 assigned negative charge : -372.8365 centred at (gu) : 90.54518 89.39916 89.35934 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6717 nv = 96 ne = 84 npr = 51115 no. pairs analyzed = 51115 no. exposed pairs = 3448 no. arc points = 24729 no. surface atoms = 1165 nbur = 1407 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3570 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2361 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1040923E-08 -3.1405998E-09 midg,1,midg; midg,igrid,midg 4.8804374E-09 1.2915219E-09 1,midg,midg; igrid,midg,midg -1.7888625E-09 8.8927123E-09 gauss-seidel spectral radius is 0.9862500 estimated iterations to convergence 70 setup time was (sec) 0.3800000 now iterating at: 17:04:45 rms-change max change #iterations 0.1206040 17.19100 at 10iterations 1.0595893E-02 1.527918 at 20iterations 9.8526559E-04 0.1905971 at 30iterations 9.1912523E-05 1.4190674E-02 at 40iterations 1.0983700E-05 1.7995834E-03 at 50iterations finished qdiffx linear iterations at : 17:04:48 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.0983700E-05 1.7995834E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 17:04:49 3.346u 0.161s 0:04.07 85.9% 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 Mon Oct 10 2011 at 17:04:49 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2572 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: 1.840396 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): 9.707000 60.87700 ymin,ymax (A): 8.746000 57.35400 zmin,zma (A): 9.040000 67.07100 x,y,z range (A): 51.17000 48.60800 58.03100 scale (grids/A): 1.840396 object centre (A): 35.29200 33.05000 38.05550 number of atom coordinates read : 2572 total number of charged atoms : 2406 net assigned charge : 4.500022 assigned positive charge : 377.3360 centred at (gu) : 91.91418 88.11761 87.70564 assigned negative charge : -372.8365 centred at (gu) : 91.63531 88.19728 88.07767 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72733 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24729 grid for indexing accessible points = 1.400000 m= 25404 mr = 49299 m= 3742 mr = 18265 m= 171 mr = 2189 m= 5 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 32257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 18872 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) : 0.6134652 object centre at (A) : 35.29200 33.05000 38.05550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0892776E-02 -2.1337613E-02 midg,1,midg; midg,igrid,midg 1.6159311E-02 1.5093950E-02 1,midg,midg; igrid,midg,midg -9.5460210E-03 9.1954451E-03 gauss-seidel spectral radius is 0.9985495 estimated iterations to convergence 208 setup time was (sec) 0.5700000 now iterating at: 17:04:50 rms-change max change #iterations 3.928495 150.8221 at 10iterations 1.793432 59.37285 at 20iterations 0.8209568 29.03842 at 30iterations 0.3751652 12.87152 at 40iterations 0.1709921 6.428187 at 50iterations 7.8207783E-02 2.640722 at 60iterations 3.5893206E-02 1.187873 at 70iterations 1.6416555E-02 0.5659962 at 80iterations 7.4989265E-03 0.2468677 at 90iterations 3.4251998E-03 0.1045971 at 100iterations 1.5744481E-03 5.3105354E-02 at 110iterations 7.1797497E-04 2.3502350E-02 at 120iterations finished qdiffx linear iterations at : 17:04:57 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 7.1797497E-04 2.3502350E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 17:04:57 7.693u 0.196s 0:08.47 93.0% 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 17:04:58 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2572 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: 2.760594 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): 9.707000 60.87700 ymin,ymax (A): 8.746000 57.35400 zmin,zma (A): 9.040000 67.07100 x,y,z range (A): 51.17000 48.60800 58.03100 scale (grids/A): 2.760594 object centre (A): 35.29200 33.05000 38.05550 number of atom coordinates read : 2572 total number of charged atoms : 2406 net assigned charge : 4.500022 assigned positive charge : 377.3360 centred at (gu) : 92.87111 87.17629 86.55829 assigned negative charge : -372.8365 centred at (gu) : 92.45287 87.29583 87.11649 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 168282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24729 grid for indexing accessible points = 1.400000 m= 83055 mr = 119941 m= 29112 mr = 66977 m= 6426 mr = 22897 m= 713 mr = 4644 m= 45 mr = 410 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9100000 number of dielectric boundary points 72747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 19247 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) : 1.840396 object centre at (A) : 35.29200 33.05000 38.05550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6692458 -0.2149888 midg,1,midg; midg,igrid,midg 0.1179917 0.1487186 1,midg,midg; igrid,midg,midg -0.1415111 0.1038274 gauss-seidel spectral radius is 0.9992424 estimated iterations to convergence 287 setup time was (sec) 1.130000 now iterating at: 17:04:59 rms-change max change #iterations 9.294707 273.2005 at 10iterations 5.405077 123.5283 at 20iterations 3.104461 71.56731 at 30iterations 1.786385 40.51022 at 40iterations 1.025538 19.22371 at 50iterations 0.5857916 12.18130 at 60iterations 0.3349712 6.683128 at 70iterations 0.1915125 3.764232 at 80iterations 0.1093252 2.200793 at 90iterations 6.2291045E-02 1.224613 at 100iterations 3.5550244E-02 0.6128502 at 110iterations 2.0315658E-02 0.3915939 at 120iterations 1.1586551E-02 0.2122040 at 130iterations 6.6114380E-03 0.1347008 at 140iterations 3.7656564E-03 7.3238373E-02 at 150iterations 2.1505908E-03 3.9822102E-02 at 160iterations 1.2274509E-03 2.3380280E-02 at 170iterations 6.9937762E-04 1.3631821E-02 at 180iterations finished qdiffx linear iterations at : 17:05:10 total time elapsed so far: 12.30000 # loops : 180 mean,max change (kT/e) : 6.9937762E-04 1.3631821E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 17:05:11 12.424u 0.231s 0:13.80 91.6% 0+0k 0+0io 0pf+0w