Sat Oct 8 19:42:09 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 19:42:09 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 has a net charge of 0.5140 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: 0.6165890 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): -10.67200 38.80200 ymin,ymax (A): -22.57900 25.57600 zmin,zma (A): -12.46600 45.27100 x,y,z range (A): 49.47400 48.15500 57.73700 scale (grids/A): 0.6165890 object centre (A): 14.06500 1.498500 16.40250 number of atom coordinates read : 2576 total number of charged atoms : 2453 net assigned charge : 3.542005 assigned positive charge : 393.7300 centred at (gu) : 88.55151 89.15372 89.55808 assigned negative charge : -390.1886 centred at (gu) : 88.45950 89.20242 89.44690 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6368 nv = 96 ne = 84 npr = 53679 no. pairs analyzed = 53679 no. exposed pairs = 3029 no. arc points = 21786 no. surface atoms = 1015 nbur = 1561 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 3516 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 66 time to turn everything in is 0.1900000 number of dielectric boundary points 3164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2161 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7971 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5747308E-09 8.4171266E-09 midg,1,midg; midg,igrid,midg 6.7345680E-09 -2.1830723E-10 1,midg,midg; igrid,midg,midg -4.1553951E-09 5.9291949E-09 gauss-seidel spectral radius is 0.9863735 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 19:42:10 rms-change max change #iterations 0.1208163 20.06838 at 10iterations 1.0972007E-02 1.485067 at 20iterations 9.9918025E-04 0.1539803 at 30iterations 9.2626506E-05 1.3549805E-02 at 40iterations 8.2891975E-06 1.2912750E-03 at 50iterations finished qdiffx linear iterations at : 19:42:13 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 8.2891975E-06 1.2912750E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 19:42:13 3.561u 0.198s 0:04.02 93.2% 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 19:42:13 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 has a net charge of 0.5140 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: 1.849767 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): -10.67200 38.80200 ymin,ymax (A): -22.57900 25.57600 zmin,zma (A): -12.46600 45.27100 x,y,z range (A): 49.47400 48.15500 57.73700 scale (grids/A): 1.849767 object centre (A): 14.06500 1.498500 16.40250 number of atom coordinates read : 2576 total number of charged atoms : 2453 net assigned charge : 3.542005 assigned positive charge : 393.7300 centred at (gu) : 85.65396 87.46078 88.67391 assigned negative charge : -390.1886 centred at (gu) : 85.37799 87.60728 88.34035 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21786 grid for indexing accessible points = 1.400000 m= 23982 mr = 48219 m= 3373 mr = 17558 m= 168 mr = 2033 m= 0 mr = 37 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4031 time to turn everything in is 0.3600000 number of dielectric boundary points 29034 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19216 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) : 0.6165890 object centre at (A) : 14.06500 1.498500 16.40250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1276437E-03 2.4335204E-02 midg,1,midg; midg,igrid,midg 9.1261780E-03 1.6040129E-03 1,midg,midg; igrid,midg,midg -2.8360218E-03 3.1009991E-02 gauss-seidel spectral radius is 0.9985492 estimated iterations to convergence 208 setup time was (sec) 0.5800000 now iterating at: 19:42:14 rms-change max change #iterations 3.985385 166.6841 at 10iterations 1.821592 62.23746 at 20iterations 0.8321586 27.19186 at 30iterations 0.3801030 12.31810 at 40iterations 0.1741236 5.437150 at 50iterations 7.9916753E-02 2.572559 at 60iterations 3.6491584E-02 1.278128 at 70iterations 1.6651168E-02 0.5401831 at 80iterations 7.6631662E-03 0.2587681 at 90iterations 3.4967463E-03 0.1149483 at 100iterations 1.6000307E-03 5.0235748E-02 at 110iterations 7.3319831E-04 2.4147034E-02 at 120iterations finished qdiffx linear iterations at : 19:42:22 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 7.3319831E-04 2.4147034E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 19:42:22 8.093u 0.223s 0:08.59 96.7% 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 19:42:22 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 has a net charge of 0.5140 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: 2.774651 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): -10.67200 38.80200 ymin,ymax (A): -22.57900 25.57600 zmin,zma (A): -12.46600 45.27100 x,y,z range (A): 49.47400 48.15500 57.73700 scale (grids/A): 2.774651 object centre (A): 14.06500 1.498500 16.40250 number of atom coordinates read : 2576 total number of charged atoms : 2453 net assigned charge : 3.542005 assigned positive charge : 393.7300 centred at (gu) : 83.48081 86.19113 88.01061 assigned negative charge : -390.1886 centred at (gu) : 83.06703 86.41093 87.51045 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 160710 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21786 grid for indexing accessible points = 1.400000 m= 79050 mr = 116910 m= 26672 mr = 64695 m= 5931 mr = 21323 m= 716 mr = 4290 m= 36 mr = 437 m= 0 mr = 11 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 13419 time to turn everything in is 0.9000000 number of dielectric boundary points 65449 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 19620 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) : 1.849767 object centre at (A) : 14.06500 1.498500 16.40250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8414883E-02 0.2955193 midg,1,midg; midg,igrid,midg 0.1192062 2.8320711E-02 1,midg,midg; igrid,midg,midg -3.0839976E-02 0.4238392 gauss-seidel spectral radius is 0.9992290 estimated iterations to convergence 284 setup time was (sec) 1.170000 now iterating at: 19:42:23 rms-change max change #iterations 9.406086 302.8029 at 10iterations 5.396724 129.4136 at 20iterations 3.075449 72.34982 at 30iterations 1.751383 41.61134 at 40iterations 0.9967595 22.40726 at 50iterations 0.5664915 11.84621 at 60iterations 0.3220325 6.646857 at 70iterations 0.1828787 4.012283 at 80iterations 0.1039699 1.874554 at 90iterations 5.9027802E-02 1.086769 at 100iterations 3.3494715E-02 0.8098831 at 110iterations 1.9008944E-02 0.3601737 at 120iterations 1.0790509E-02 0.2017069 at 130iterations 6.1171525E-03 0.1206876 at 140iterations 3.4718162E-03 6.5448761E-02 at 150iterations 1.9681626E-03 3.5968661E-02 at 160iterations 1.1172676E-03 2.0952463E-02 at 170iterations 6.3230109E-04 1.2586117E-02 at 180iterations finished qdiffx linear iterations at : 19:42:36 total time elapsed so far: 13.31000 # loops : 180 mean,max change (kT/e) : 6.3230109E-04 1.2586117E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 19:42:36 13.449u 0.238s 0:14.04 97.3% 0+0k 0+0io 0pf+0w