Sun Oct 9 14:19:45 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 Sun Oct 9 2011 at 14:19:45 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 !!! WARNING: HIQ 135 has a net charge of 0.5140 !!! WARNING: SEP 281 has a net charge of -0.4750 !!! WARNING: SEP 286 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6134124 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): -30.67000 17.82900 ymin,ymax (A): -31.40500 22.73900 zmin,zma (A): -13.48100 44.55500 x,y,z range (A): 48.49900 54.14400 58.03600 scale (grids/A): 0.6134124 object centre (A): -6.420500 -4.333000 15.53700 number of atom coordinates read : 2783 total number of charged atoms : 2638 net assigned charge : 2.064007 assigned positive charge : 423.9234 centred at (gu) : 90.64662 89.80351 89.24354 assigned negative charge : -421.8604 centred at (gu) : 90.76628 89.89209 89.18228 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6882 nv = 96 ne = 84 npr = 56026 no. pairs analyzed = 56026 no. exposed pairs = 3517 no. arc points = 24464 no. surface atoms = 1190 nbur = 1593 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 3641 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2457 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8537 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6723141E-09 4.2714188E-09 midg,1,midg; midg,igrid,midg 6.9530914E-09 -3.7181029E-09 1,midg,midg; igrid,midg,midg 7.3197488E-09 -6.7151902E-09 gauss-seidel spectral radius is 0.9862566 estimated iterations to convergence 70 setup time was (sec) 0.4200000 now iterating at: 14:19:45 rms-change max change #iterations 0.1254814 21.07556 at 10iterations 1.1233787E-02 2.001270 at 20iterations 1.0645483E-03 0.1721878 at 30iterations 1.0419537E-04 1.6315460E-02 at 40iterations 1.4889381E-05 2.2888184E-03 at 50iterations finished qdiffx linear iterations at : 14:19:48 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.4889381E-05 2.2888184E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 14:19:49 3.431u 0.153s 0:03.86 92.7% 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 Sun Oct 9 2011 at 14:19:49 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 !!! WARNING: HIQ 135 has a net charge of 0.5140 !!! WARNING: SEP 281 has a net charge of -0.4750 !!! WARNING: SEP 286 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.840237 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): -30.67000 17.82900 ymin,ymax (A): -31.40500 22.73900 zmin,zma (A): -13.48100 44.55500 x,y,z range (A): 48.49900 54.14400 58.03600 scale (grids/A): 1.840237 object centre (A): -6.420500 -4.333000 15.53700 number of atom coordinates read : 2783 total number of charged atoms : 2638 net assigned charge : 2.064007 assigned positive charge : 423.9234 centred at (gu) : 91.93939 89.40997 87.72986 assigned negative charge : -421.8604 centred at (gu) : 92.29883 89.67600 87.54638 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24464 grid for indexing accessible points = 1.400000 m= 25697 mr = 50493 m= 3705 mr = 18242 m= 206 mr = 2096 m= 2 mr = 75 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 0.3700000 number of dielectric boundary points 33117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 20608 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) : 0.6134124 object centre at (A) : -6.420500 -4.333000 15.53700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8418172E-02 -4.7448035E-03 midg,1,midg; midg,igrid,midg 8.0949310E-03 1.0966389E-02 1,midg,midg; igrid,midg,midg 1.3725433E-02 8.3407639E-03 gauss-seidel spectral radius is 0.9985639 estimated iterations to convergence 209 setup time was (sec) 0.5800000 now iterating at: 14:19:49 rms-change max change #iterations 4.163060 169.7276 at 10iterations 1.902060 71.52582 at 20iterations 0.8710209 29.13654 at 30iterations 0.3996672 12.96748 at 40iterations 0.1836875 6.100172 at 50iterations 8.4147267E-02 2.964947 at 60iterations 3.8659982E-02 1.281198 at 70iterations 1.7840018E-02 0.5372682 at 80iterations 8.1842327E-03 0.2415037 at 90iterations 3.7553450E-03 0.1202583 at 100iterations 1.7347456E-03 5.2776337E-02 at 110iterations 7.9667312E-04 2.6412964E-02 at 120iterations finished qdiffx linear iterations at : 14:19:56 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 7.9667312E-04 2.6412964E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 14:19:57 7.830u 0.220s 0:08.33 96.6% 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 14:19:57 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 !!! WARNING: HIQ 135 has a net charge of 0.5140 !!! WARNING: SEP 281 has a net charge of -0.4750 !!! WARNING: SEP 286 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.760356 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): -30.67000 17.82900 ymin,ymax (A): -31.40500 22.73900 zmin,zma (A): -13.48100 44.55500 x,y,z range (A): 48.49900 54.14400 58.03600 scale (grids/A): 2.760356 object centre (A): -6.420500 -4.333000 15.53700 number of atom coordinates read : 2783 total number of charged atoms : 2638 net assigned charge : 2.064007 assigned positive charge : 423.9234 centred at (gu) : 92.90903 89.11488 86.59454 assigned negative charge : -421.8604 centred at (gu) : 93.44806 89.51407 86.31948 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 172342 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24464 grid for indexing accessible points = 1.400000 m= 84521 mr = 123266 m= 28939 mr = 67625 m= 6366 mr = 22399 m= 847 mr = 4496 m= 54 mr = 566 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9500000 number of dielectric boundary points 74697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 21097 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) : 1.840237 object centre at (A) : -6.420500 -4.333000 15.53700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7151275 -2.9201636E-03 midg,1,midg; midg,igrid,midg 7.2493486E-02 0.1494574 1,midg,midg; igrid,midg,midg 9.2570968E-02 9.2487946E-02 gauss-seidel spectral radius is 0.9992433 estimated iterations to convergence 287 setup time was (sec) 1.180000 now iterating at: 14:19:58 rms-change max change #iterations 10.04041 316.2653 at 10iterations 5.951838 161.8921 at 20iterations 3.475947 71.73856 at 30iterations 2.022188 46.95676 at 40iterations 1.171138 25.19888 at 50iterations 0.6778541 15.63185 at 60iterations 0.3899325 8.258787 at 70iterations 0.2245891 4.350078 at 80iterations 0.1287929 2.518738 at 90iterations 7.4035816E-02 1.401585 at 100iterations 4.2453840E-02 0.7972870 at 110iterations 2.4347562E-02 0.4750404 at 120iterations 1.3922339E-02 0.2604671 at 130iterations 7.9829888E-03 0.1567926 at 140iterations 4.5702611E-03 8.3538815E-02 at 150iterations 2.6253981E-03 5.1467896E-02 at 160iterations 1.5088947E-03 2.9680252E-02 at 170iterations 8.6917204E-04 1.6157150E-02 at 180iterations finished qdiffx linear iterations at : 14:20:10 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 8.6917204E-04 1.6157150E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 14:20:10 12.724u 0.208s 0:13.21 97.8% 0+0k 0+0io 0pf+0w