Tue Oct 11 06:10:13 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 Tue Oct 11 2011 at 06:10:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2008 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7496474 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): 0.7620000 41.14000 ymin,ymax (A): -26.14200 17.69400 zmin,zma (A): 38.42100 85.91000 x,y,z range (A): 40.37800 43.83600 47.48899 scale (grids/A): 0.7496474 object centre (A): 20.95100 -4.224000 62.16550 number of atom coordinates read : 2008 total number of charged atoms : 1880 net assigned charge : 6.500006 assigned positive charge : 302.9601 centred at (gu) : 88.74185 89.96407 91.13470 assigned negative charge : -296.4602 centred at (gu) : 88.69643 90.15436 91.20497 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7842 nv = 96 ne = 84 npr = 40355 no. pairs analyzed = 40355 no. exposed pairs = 2468 no. arc points = 16918 no. surface atoms = 840 nbur = 1168 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 598 mr = 4555 m= 5 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1448 ## 139 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8216 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8076015E-07 7.4392752E-08 midg,1,midg; midg,igrid,midg 3.5776293E-07 -7.7790531E-08 1,midg,midg; igrid,midg,midg 1.1235831E-07 1.5468709E-07 gauss-seidel spectral radius is 0.9907107 estimated iterations to convergence 84 setup time was (sec) 0.5100000 now iterating at: 06:10:14 rms-change max change #iterations 0.2493093 43.69517 at 10iterations 3.5119861E-02 4.987932 at 20iterations 4.9392516E-03 0.6573524 at 30iterations 7.6075306E-04 0.1055450 at 40iterations 1.4926461E-04 1.7070770E-02 at 50iterations finished qdiffx linear iterations at : 06:10:17 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.4926461E-04 1.7070770E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 06:10:17 3.344u 0.140s 0:04.07 85.5% 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 Tue Oct 11 2011 at 06:10:18 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 = 2008 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.248942 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): 0.7620000 41.14000 ymin,ymax (A): -26.14200 17.69400 zmin,zma (A): 38.42100 85.91000 x,y,z range (A): 40.37800 43.83600 47.48899 scale (grids/A): 2.248942 object centre (A): 20.95100 -4.224000 62.16550 number of atom coordinates read : 2008 total number of charged atoms : 1880 net assigned charge : 6.500006 assigned positive charge : 302.9601 centred at (gu) : 86.22555 89.89220 93.40428 assigned negative charge : -296.4602 centred at (gu) : 86.08950 90.46329 93.61497 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 82122 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16918 grid for indexing accessible points = 1.400000 m= 35508 mr = 58533 m= 8039 mr = 27529 m= 989 mr = 5689 m= 56 mr = 601 m= 0 mr = 13 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 34349 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 14985 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) : 0.7496474 object centre at (A) : 20.95100 -4.224000 62.16550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4103989E-02 1.9528648E-02 midg,1,midg; midg,igrid,midg 8.1813522E-02 8.0019226E-03 1,midg,midg; igrid,midg,midg 4.1304562E-02 1.4699395E-02 gauss-seidel spectral radius is 0.9989350 estimated iterations to convergence 242 setup time was (sec) 1.010000 now iterating at: 06:10:19 rms-change max change #iterations 4.975628 241.4844 at 10iterations 2.557877 84.46175 at 20iterations 1.313531 37.34524 at 30iterations 0.6762622 19.33760 at 40iterations 0.3477511 10.76166 at 50iterations 0.1783708 4.944221 at 60iterations 9.1533631E-02 2.762719 at 70iterations 4.7029302E-02 1.389422 at 80iterations 2.4125971E-02 0.7227058 at 90iterations 1.2435833E-02 0.3545508 at 100iterations 6.4268974E-03 0.1992054 at 110iterations 3.3251997E-03 0.1010056 at 120iterations finished qdiffx linear iterations at : 06:10:26 total time elapsed so far: 8.540000 # loops : 120 mean,max change (kT/e) : 3.3251997E-03 0.1010056 energy calculations done at 8.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.720000 DelPhi exited at 06:10:27 8.727u 0.271s 0:09.31 96.5% 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 Tue Oct 11 2011 at 06:10:27 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 = 2008 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: 3.373413 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): 0.7620000 41.14000 ymin,ymax (A): -26.14200 17.69400 zmin,zma (A): 38.42100 85.91000 x,y,z range (A): 40.37800 43.83600 47.48899 scale (grids/A): 3.373413 object centre (A): 20.95100 -4.224000 62.16550 number of atom coordinates read : 2008 total number of charged atoms : 1880 net assigned charge : 6.500006 assigned positive charge : 302.9601 centred at (gu) : 84.33834 89.83821 95.10649 assigned negative charge : -296.4602 centred at (gu) : 84.13430 90.69483 95.42242 start vw surface at 0.1500000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 188936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16918 grid for indexing accessible points = 1.400000 m= 107174 mr = 140521 m= 47942 mr = 90148 m= 15637 mr = 40264 m= 3748 mr = 12471 m= 683 mr = 2887 m= 35 mr = 537 m= 0 mr = 12 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.080000 number of dielectric boundary points 77315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.210000 number of grid points assigned charge 15040 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) : 2.248942 object centre at (A) : 20.95100 -4.224000 62.16550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3471262 0.1515290 midg,1,midg; midg,igrid,midg 0.5804977 4.2544376E-02 1,midg,midg; igrid,midg,midg 0.4508555 6.6739269E-02 gauss-seidel spectral radius is 0.9993243 estimated iterations to convergence 303 setup time was (sec) 2.370000 now iterating at: 06:10:29 rms-change max change #iterations 10.82862 305.8114 at 10iterations 6.495049 133.5721 at 20iterations 3.879324 67.79250 at 30iterations 2.317060 43.46189 at 40iterations 1.380604 24.49252 at 50iterations 0.8187706 14.54307 at 60iterations 0.4868699 8.593936 at 70iterations 0.2880822 4.979202 at 80iterations 0.1708282 2.739406 at 90iterations 0.1014207 1.619591 at 100iterations 6.0011804E-02 1.100098 at 110iterations 3.5550311E-02 0.5705166 at 120iterations 2.1184307E-02 0.3456688 at 130iterations 1.2668249E-02 0.1977973 at 140iterations 7.6866932E-03 0.1302948 at 150iterations 4.7595431E-03 7.8215122E-02 at 160iterations 3.0475059E-03 5.5355072E-02 at 170iterations 2.0589142E-03 4.0939331E-02 at 180iterations finished qdiffx linear iterations at : 06:10:40 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 2.0589142E-03 4.0939331E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 06:10:40 12.844u 0.161s 0:13.47 96.5% 0+0k 0+0io 0pf+0w