Sat Oct 8 16:52:42 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 16:52:42 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3570 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: 0.5607712 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): 15.26600 78.75000 ymin,ymax (A): 127.7080 183.3110 zmin,zma (A): -1.440000 59.80100 x,y,z range (A): 63.48400 55.60299 61.24100 scale (grids/A): 0.5607712 object centre (A): 47.00800 155.5095 29.18050 number of atom coordinates read : 3570 total number of charged atoms : 3452 net assigned charge : -1.499980 assigned positive charge : 544.4695 centred at (gu) : 91.39217 89.31793 88.30659 assigned negative charge : -545.9709 centred at (gu) : 91.37221 89.15494 88.33970 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7445 nv = 96 ne = 84 npr = 70044 no. pairs analyzed = 70044 no. exposed pairs = 4801 no. arc points = 32980 no. surface atoms = 1607 nbur = 1963 mkacc time = 0.1600000 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 = 1.512000 m= 349 mr = 3832 m= 0 mr = 22 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3301 ## 377 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9627 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6385940E-10 -4.1199477E-10 midg,1,midg; midg,igrid,midg -2.9194815E-09 1.7454862E-09 1,midg,midg; igrid,midg,midg -3.1167305E-10 1.7300383E-10 gauss-seidel spectral radius is 0.9836476 estimated iterations to convergence 64 setup time was (sec) 0.5700000 now iterating at: 16:52:43 rms-change max change #iterations 9.6519679E-02 16.57816 at 10iterations 6.7705014E-03 1.021408 at 20iterations 5.0665822E-04 8.5292816E-02 at 30iterations 7.5670258E-05 1.0992050E-02 at 40iterations 3.3494169E-05 4.9381256E-03 at 50iterations finished qdiffx linear iterations at : 16:52:47 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 3.3494169E-05 4.9381256E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 16:52:48 3.162u 0.175s 0:05.78 57.6% 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 Sat Oct 8 2011 at 16:52:48 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3570 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: 1.682314 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): 15.26600 78.75000 ymin,ymax (A): 127.7080 183.3110 zmin,zma (A): -1.440000 59.80100 x,y,z range (A): 63.48400 55.60299 61.24100 scale (grids/A): 1.682314 object centre (A): 47.00800 155.5095 29.18050 number of atom coordinates read : 3570 total number of charged atoms : 3452 net assigned charge : -1.499980 assigned positive charge : 544.4695 centred at (gu) : 94.17558 87.95287 84.91888 assigned negative charge : -545.9709 centred at (gu) : 94.11622 87.46437 85.01891 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81736 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32980 grid for indexing accessible points = 1.400000 m= 25816 mr = 55092 m= 3142 mr = 17393 m= 125 mr = 1588 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 36719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 320 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 26618 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) : 0.5607712 object centre at (A) : 47.00800 155.5095 29.18050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2634473E-03 9.8734125E-03 midg,1,midg; midg,igrid,midg -2.2381628E-02 1.8937275E-02 1,midg,midg; igrid,midg,midg -1.1162449E-02 -2.0899218E-02 gauss-seidel spectral radius is 0.9983681 estimated iterations to convergence 196 setup time was (sec) 0.8200000 now iterating at: 16:52:49 rms-change max change #iterations 4.013333 163.8112 at 10iterations 1.750507 58.76510 at 20iterations 0.7636703 22.83691 at 30iterations 0.3339618 11.76603 at 40iterations 0.1459009 5.400341 at 50iterations 6.3904539E-02 2.001780 at 60iterations 2.7797699E-02 0.9411268 at 70iterations 1.2157147E-02 0.3893490 at 80iterations 5.3286194E-03 0.1824570 at 90iterations 2.3277772E-03 7.8201294E-02 at 100iterations 1.0179139E-03 3.1742096E-02 at 110iterations 4.4714319E-04 1.3093203E-02 at 120iterations finished qdiffx linear iterations at : 16:52:55 total time elapsed so far: 7.020000 # loops : 120 mean,max change (kT/e) : 4.4714319E-04 1.3093203E-02 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.190000 DelPhi exited at 16:52:55 7.195u 0.186s 0:07.71 95.5% 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 Sat Oct 8 2011 at 16:52:56 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3570 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: 2.523470 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): 15.26600 78.75000 ymin,ymax (A): 127.7080 183.3110 zmin,zma (A): -1.440000 59.80100 x,y,z range (A): 63.48400 55.60299 61.24100 scale (grids/A): 2.523470 object centre (A): 47.00800 155.5095 29.18050 number of atom coordinates read : 3570 total number of charged atoms : 3452 net assigned charge : -1.499980 assigned positive charge : 544.4695 centred at (gu) : 96.26304 86.92924 82.37803 assigned negative charge : -545.9709 centred at (gu) : 96.17406 86.19643 82.52825 start vw surface at 0.1800000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 190087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32980 grid for indexing accessible points = 1.400000 m= 87969 mr = 135509 m= 26465 mr = 68365 m= 5087 mr = 19671 m= 512 mr = 3416 m= 14 mr = 285 m= 1 mr = 3 m= 1 mr = 0 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 82888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 27595 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) : 1.682314 object centre at (A) : 47.00800 155.5095 29.18050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2258472 0.2688586 midg,1,midg; midg,igrid,midg -0.3203906 0.3031506 1,midg,midg; igrid,midg,midg -0.1910098 -0.3611661 gauss-seidel spectral radius is 0.9992186 estimated iterations to convergence 282 setup time was (sec) 1.670000 now iterating at: 16:52:57 rms-change max change #iterations 10.24676 264.6662 at 10iterations 6.011575 142.8238 at 20iterations 3.497592 83.83898 at 30iterations 2.018687 49.69253 at 40iterations 1.159286 25.61834 at 50iterations 0.6646416 12.48123 at 60iterations 0.3800323 7.557335 at 70iterations 0.2164682 3.799850 at 80iterations 0.1233968 2.289330 at 90iterations 7.0139587E-02 1.424547 at 100iterations 3.9872922E-02 0.7158203 at 110iterations 2.2611413E-02 0.4072781 at 120iterations 1.2858505E-02 0.2459335 at 130iterations 7.2816694E-03 0.1255531 at 140iterations 4.1332250E-03 7.7018261E-02 at 150iterations 2.3434083E-03 4.3898582E-02 at 160iterations 1.3301134E-03 2.7330399E-02 at 170iterations 7.5408496E-04 1.3485432E-02 at 180iterations finished qdiffx linear iterations at : 16:53:08 total time elapsed so far: 12.07000 # loops : 180 mean,max change (kT/e) : 7.5408496E-04 1.3485432E-02 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 16:53:08 12.247u 0.197s 0:12.72 97.7% 0+0k 0+0io 0pf+0w