Wed Feb 15 08:55:32 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:32 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3690 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5885465 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): 14.97300 75.46100 ymin,ymax (A): -48.61900 9.901000 zmin,zma (A): 74.41400 132.7870 x,y,z range (A): 60.48800 58.52000 58.37299 scale (grids/A): 0.5885465 object centre (A): 45.21700 -19.35900 103.6005 number of atom coordinates read : 3690 total number of charged atoms : 3622 net assigned charge : -2.499984 assigned positive charge : 570.6261 centred at (gu) : 90.31406 89.83324 90.58729 assigned negative charge : -573.1282 centred at (gu) : 90.17425 89.82511 90.52110 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8289 nv = 96 ne = 84 npr = 74958 no. pairs analyzed = 74958 no. exposed pairs = 4342 no. arc points = 30116 no. surface atoms = 1470 nbur = 2220 mkacc time = 0.1700000 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 = 1.456000 m= 390 mr = 4600 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.4100000 number of dielectric boundary points 4047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3178 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10871 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8511484E-09 1.9629987E-09 midg,1,midg; midg,igrid,midg -1.1089875E-09 -4.4143203E-10 1,midg,midg; igrid,midg,midg -5.6675806E-09 4.7426516E-09 gauss-seidel spectral radius is 0.9851518 estimated iterations to convergence 67 setup time was (sec) 0.6600000 now iterating at: 08:55:33 rms-change max change #iterations 0.1225137 16.98997 at 10iterations 1.0011259E-02 1.321033 at 20iterations 8.1869186E-04 0.1152420 at 30iterations 6.8288682E-05 1.0608673E-02 at 40iterations 5.9644303E-06 8.8882446E-04 at 50iterations finished qdiffx linear iterations at : 08:55:36 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 5.9644303E-06 8.8882446E-04 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 08:55:37 3.737u 0.184s 0:04.86 80.4% 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 Wed Feb 15 2012 at 08:55:37 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3690 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: 1.765640 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): 14.97300 75.46100 ymin,ymax (A): -48.61900 9.901000 zmin,zma (A): 74.41400 132.7870 x,y,z range (A): 60.48800 58.52000 58.37299 scale (grids/A): 1.765640 object centre (A): 45.21700 -19.35900 103.6005 number of atom coordinates read : 3690 total number of charged atoms : 3622 net assigned charge : -2.499984 assigned positive charge : 570.6261 centred at (gu) : 90.94061 89.49849 91.76066 assigned negative charge : -573.1282 centred at (gu) : 90.52200 89.47466 91.56281 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 92389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30116 grid for indexing accessible points = 1.400000 m= 30240 mr = 65083 m= 3757 mr = 21994 m= 144 mr = 2179 m= 0 mr = 34 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 3280 time to turn everything in is 0.6600000 number of dielectric boundary points 37240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 28173 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) : 0.5885465 object centre at (A) : 45.21700 -19.35900 103.6005 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9446885E-03 2.6514167E-02 midg,1,midg; midg,igrid,midg -3.7333705E-03 1.8430211E-03 1,midg,midg; igrid,midg,midg -3.5232682E-02 1.1366879E-03 gauss-seidel spectral radius is 0.9985201 estimated iterations to convergence 206 setup time was (sec) 0.9600000 now iterating at: 08:55:38 rms-change max change #iterations 4.538918 180.3573 at 10iterations 2.059695 66.61997 at 20iterations 0.9361894 28.76834 at 30iterations 0.4247579 12.77688 at 40iterations 0.1928205 5.257969 at 50iterations 8.7396234E-02 2.890358 at 60iterations 3.9708540E-02 1.320816 at 70iterations 1.8049149E-02 0.5004148 at 80iterations 8.2129668E-03 0.2378960 at 90iterations 3.7216062E-03 0.1161537 at 100iterations 1.6926951E-03 5.3581238E-02 at 110iterations 7.6828140E-04 2.1810532E-02 at 120iterations finished qdiffx linear iterations at : 08:55:45 total time elapsed so far: 8.360000 # loops : 120 mean,max change (kT/e) : 7.6828140E-04 2.1810532E-02 energy calculations done at 8.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.560000 DelPhi exited at 08:55:47 8.564u 0.244s 0:09.70 90.7% 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 Wed Feb 15 2012 at 08:55:47 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3690 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.648459 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): 14.97300 75.46100 ymin,ymax (A): -48.61900 9.901000 zmin,zma (A): 74.41400 132.7870 x,y,z range (A): 60.48800 58.52000 58.37299 scale (grids/A): 2.648459 object centre (A): 45.21700 -19.35900 103.6005 number of atom coordinates read : 3690 total number of charged atoms : 3622 net assigned charge : -2.499984 assigned positive charge : 570.6261 centred at (gu) : 91.41074 89.24749 92.64063 assigned negative charge : -573.1282 centred at (gu) : 90.78291 89.21193 92.34427 start vw surface at 0.2300000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 214768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30116 grid for indexing accessible points = 1.400000 m= 103107 mr = 158606 m= 32451 mr = 84196 m= 6410 mr = 25552 m= 606 mr = 4603 m= 19 mr = 339 m= 0 mr = 6 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 11180 time to turn everything in is 1.740000 number of dielectric boundary points 84059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 28969 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) : 1.765640 object centre at (A) : 45.21700 -19.35900 103.6005 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1251371 0.4121199 midg,1,midg; midg,igrid,midg 4.8298651E-05 -9.5494045E-03 1,midg,midg; igrid,midg,midg -0.4914612 -0.1844400 gauss-seidel spectral radius is 0.9992541 estimated iterations to convergence 289 setup time was (sec) 2.080000 now iterating at: 08:55:49 rms-change max change #iterations 11.02540 290.9747 at 10iterations 6.425784 150.2478 at 20iterations 3.712459 75.41673 at 30iterations 2.142310 48.99903 at 40iterations 1.235796 24.53491 at 50iterations 0.7094100 12.26391 at 60iterations 0.4073874 8.202122 at 70iterations 0.2336535 4.256569 at 80iterations 0.1340528 2.602783 at 90iterations 7.6691210E-02 1.370770 at 100iterations 4.4048347E-02 0.7481194 at 110iterations 2.5241381E-02 0.4418840 at 120iterations 1.4434996E-02 0.2574120 at 130iterations 8.2937330E-03 0.1483631 at 140iterations 4.7382154E-03 8.1506729E-02 at 150iterations 2.7168447E-03 4.3689728E-02 at 160iterations 1.5558482E-03 2.6812553E-02 at 170iterations 8.9196744E-04 1.4219284E-02 at 180iterations finished qdiffx linear iterations at : 08:56:01 total time elapsed so far: 14.12000 # loops : 180 mean,max change (kT/e) : 8.9196744E-04 1.4219284E-02 energy calculations done at 14.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.31000 DelPhi exited at 08:56:02 14.311u 0.205s 0:14.95 97.0% 0+0k 0+0io 0pf+0w