Sun Oct 9 19:31:56 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 Sun Oct 9 2011 at 19:31:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3053 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5189655 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): -3.137000 65.46100 ymin,ymax (A): -13.64100 35.11400 zmin,zma (A): 18.81300 71.04800 x,y,z range (A): 68.59800 48.75500 52.23500 scale (grids/A): 0.5189655 object centre (A): 31.16200 10.73650 44.93050 number of atom coordinates read : 3053 total number of charged atoms : 2910 net assigned charge : 11.50003 assigned positive charge : 462.9442 centred at (gu) : 89.94579 89.82933 89.79854 assigned negative charge : -451.4454 centred at (gu) : 90.04621 89.88338 89.78186 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5345 nv = 96 ne = 84 npr = 59933 no. pairs analyzed = 59933 no. exposed pairs = 3988 no. arc points = 28227 no. surface atoms = 1322 nbur = 1731 mkacc time = 0.1400000 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 = 1.652000 m= 212 mr = 2688 m= 3 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 2870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2786 ## 420 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7080 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0688799E-10 2.6090580E-10 midg,1,midg; midg,igrid,midg 3.7713591E-10 1.0434686E-10 1,midg,midg; igrid,midg,midg 4.7359366E-10 -1.5883783E-12 gauss-seidel spectral radius is 0.9808860 estimated iterations to convergence 60 setup time was (sec) 0.5800000 now iterating at: 19:31:57 rms-change max change #iterations 5.6320034E-02 11.42576 at 10iterations 3.3253045E-03 0.6020622 at 20iterations 3.6251452E-04 7.2893143E-02 at 30iterations 1.1964285E-04 1.9796371E-02 at 40iterations 4.9151316E-05 7.9152584E-03 at 50iterations finished qdiffx linear iterations at : 19:32:00 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 4.9151316E-05 7.9152584E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 19:32:00 3.378u 0.146s 0:03.80 92.3% 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 Sun Oct 9 2011 at 19:32:00 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 = 3053 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.556897 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): -3.137000 65.46100 ymin,ymax (A): -13.64100 35.11400 zmin,zma (A): 18.81300 71.04800 x,y,z range (A): 68.59800 48.75500 52.23500 scale (grids/A): 1.556897 object centre (A): 31.16200 10.73650 44.93050 number of atom coordinates read : 3053 total number of charged atoms : 2910 net assigned charge : 11.50003 assigned positive charge : 462.9442 centred at (gu) : 89.83691 89.48681 89.39476 assigned negative charge : -451.4454 centred at (gu) : 90.13863 89.64967 89.34560 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 60001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28227 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 18717 mr = 40391 m= 1814 mr = 12539 m= 58 mr = 720 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 322 time to turn everything in is 0.4800000 number of dielectric boundary points 26940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 397 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 21998 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) : 0.5189655 object centre at (A) : 31.16200 10.73650 44.93050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3076078E-03 4.8496090E-03 midg,1,midg; midg,igrid,midg 7.0133624E-03 2.7018047E-03 1,midg,midg; igrid,midg,midg 1.9022582E-02 3.7867015E-03 gauss-seidel spectral radius is 0.9980039 estimated iterations to convergence 178 setup time was (sec) 0.7500000 now iterating at: 19:32:01 rms-change max change #iterations 2.995952 150.3493 at 10iterations 1.196600 53.24248 at 20iterations 0.4764611 19.50529 at 30iterations 0.1902485 7.594783 at 40iterations 7.6134741E-02 3.173048 at 50iterations 3.0467886E-02 1.171494 at 60iterations 1.2218592E-02 0.4524078 at 70iterations 4.9287276E-03 0.1949615 at 80iterations 2.0097927E-03 8.8716507E-02 at 90iterations 8.5292885E-04 3.2348633E-02 at 100iterations 4.0084956E-04 1.4903069E-02 at 110iterations 2.2215067E-04 8.4714890E-03 at 120iterations finished qdiffx linear iterations at : 19:32:07 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 2.2215067E-04 8.4714890E-03 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 19:32:08 7.329u 0.176s 0:07.79 96.1% 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 Sun Oct 9 2011 at 19:32:08 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 = 3053 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.335345 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): -3.137000 65.46100 ymin,ymax (A): -13.64100 35.11400 zmin,zma (A): 18.81300 71.04800 x,y,z range (A): 68.59800 48.75500 52.23500 scale (grids/A): 2.335345 object centre (A): 31.16200 10.73650 44.93050 number of atom coordinates read : 3053 total number of charged atoms : 2910 net assigned charge : 11.50003 assigned positive charge : 462.9442 centred at (gu) : 89.75507 89.23017 89.09197 assigned negative charge : -451.4454 centred at (gu) : 90.20779 89.47459 89.01833 start vw surface at 0.1600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 139276 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28227 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 65089 mr = 99270 m= 18091 mr = 50693 m= 2607 mr = 13065 m= 179 mr = 1444 m= 3 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 943 time to turn everything in is 1.090000 number of dielectric boundary points 60703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 23239 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) : 1.556897 object centre at (A) : 31.16200 10.73650 44.93050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8992777E-02 7.3395155E-02 midg,1,midg; midg,igrid,midg 0.1159362 3.6906566E-02 1,midg,midg; igrid,midg,midg 0.4002984 8.7105468E-02 gauss-seidel spectral radius is 0.9990796 estimated iterations to convergence 260 setup time was (sec) 1.370000 now iterating at: 19:32:09 rms-change max change #iterations 8.071473 290.8132 at 10iterations 4.466413 145.8908 at 20iterations 2.457474 58.53381 at 30iterations 1.346895 33.14122 at 40iterations 0.7322374 16.63518 at 50iterations 0.3993813 9.908211 at 60iterations 0.2168491 5.256980 at 70iterations 0.1174492 2.964148 at 80iterations 6.3830703E-02 1.625734 at 90iterations 3.4527015E-02 0.9086637 at 100iterations 1.8673416E-02 0.4274435 at 110iterations 1.0100880E-02 0.2355659 at 120iterations 5.4606195E-03 0.1332092 at 130iterations 2.9526558E-03 7.0718765E-02 at 140iterations 1.5969831E-03 3.8803101E-02 at 150iterations 8.6458551E-04 2.2457123E-02 at 160iterations 4.6918282E-04 1.1127472E-02 at 170iterations 2.5793581E-04 5.9442520E-03 at 180iterations finished qdiffx linear iterations at : 19:32:19 total time elapsed so far: 11.41000 # loops : 180 mean,max change (kT/e) : 2.5793581E-04 5.9442520E-03 energy calculations done at 11.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.60000 DelPhi exited at 19:32:20 11.604u 0.201s 0:12.08 97.6% 0+0k 0+0io 0pf+0w