Sat Oct 8 14:52:55 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 Sat Oct 8 2011 at 14:52:55 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 = 2990 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6388630 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): -12.23800 43.48600 ymin,ymax (A): -23.91200 22.79300 zmin,zma (A): -7.573000 47.53600 x,y,z range (A): 55.72400 46.70500 55.10900 scale (grids/A): 0.6388630 object centre (A): 15.62400 -0.5594997 19.98150 number of atom coordinates read : 2990 total number of charged atoms : 2845 net assigned charge : 1.228008 assigned positive charge : 446.9386 centred at (gu) : 88.79449 90.01250 91.78561 assigned negative charge : -445.7114 centred at (gu) : 88.71587 89.87070 91.76898 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8053 nv = 96 ne = 84 npr = 62657 no. pairs analyzed = 62657 no. exposed pairs = 3327 no. arc points = 23520 no. surface atoms = 1137 nbur = 1853 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 4695 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2273 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9791 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9353723E-10 5.8476561E-09 midg,1,midg; midg,igrid,midg -1.6729686E-08 1.9925482E-08 1,midg,midg; igrid,midg,midg -1.1006103E-08 9.1825063E-09 gauss-seidel spectral radius is 0.9873358 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 14:52:56 rms-change max change #iterations 0.1601365 21.15898 at 10iterations 1.5798107E-02 2.159258 at 20iterations 1.6157046E-03 0.2153454 at 30iterations 1.7872134E-04 2.2510529E-02 at 40iterations 2.2724174E-05 2.9525757E-03 at 50iterations finished qdiffx linear iterations at : 14:52:58 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 2.2724174E-05 2.9525757E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 14:52:59 3.130u 0.143s 0:03.54 92.3% 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 14:52:59 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 = 2990 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.916589 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): -12.23800 43.48600 ymin,ymax (A): -23.91200 22.79300 zmin,zma (A): -7.573000 47.53600 x,y,z range (A): 55.72400 46.70500 55.10900 scale (grids/A): 1.916589 object centre (A): 15.62400 -0.5594997 19.98150 number of atom coordinates read : 2990 total number of charged atoms : 2845 net assigned charge : 1.228008 assigned positive charge : 446.9386 centred at (gu) : 86.38274 90.03674 95.35638 assigned negative charge : -445.7114 centred at (gu) : 86.14746 89.61177 95.30676 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 88324 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23520 grid for indexing accessible points = 1.400000 m= 31897 mr = 63828 m= 4754 mr = 24064 m= 269 mr = 2920 m= 4 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 423 time to turn everything in is 0.5800000 number of dielectric boundary points 34338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 22379 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) : 0.6388630 object centre at (A) : 15.62400 -0.5594997 19.98150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2852663E-03 8.9633316E-03 midg,1,midg; midg,igrid,midg 1.5382994E-03 2.8259177E-02 1,midg,midg; igrid,midg,midg -3.6149897E-02 2.3339452E-02 gauss-seidel spectral radius is 0.9986829 estimated iterations to convergence 218 setup time was (sec) 0.8400000 now iterating at: 14:53:00 rms-change max change #iterations 4.666744 183.4053 at 10iterations 2.222390 63.62878 at 20iterations 1.055881 31.63108 at 30iterations 0.5022717 14.47985 at 40iterations 0.2381804 7.389315 at 50iterations 0.1131994 3.316711 at 60iterations 5.3877514E-02 1.535612 at 70iterations 2.5648333E-02 0.7785492 at 80iterations 1.2211011E-02 0.3553958 at 90iterations 5.7988735E-03 0.1805801 at 100iterations 2.7527520E-03 7.7061653E-02 at 110iterations 1.3157865E-03 3.9955139E-02 at 120iterations finished qdiffx linear iterations at : 14:53:06 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 1.3157865E-03 3.9955139E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 14:53:06 6.989u 0.181s 0:07.54 94.9% 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 14:53:06 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 = 2990 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.874883 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): -12.23800 43.48600 ymin,ymax (A): -23.91200 22.79300 zmin,zma (A): -7.573000 47.53600 x,y,z range (A): 55.72400 46.70500 55.10900 scale (grids/A): 2.874883 object centre (A): 15.62400 -0.5594997 19.98150 number of atom coordinates read : 2990 total number of charged atoms : 2845 net assigned charge : 1.228008 assigned positive charge : 446.9386 centred at (gu) : 84.57390 90.05500 98.03468 assigned negative charge : -445.7114 centred at (gu) : 84.22118 89.41754 97.95999 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 204885 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23520 grid for indexing accessible points = 1.400000 m= 104450 mr = 154243 m= 36486 mr = 87107 m= 8432 mr = 29546 m= 1167 mr = 6170 m= 64 mr = 778 m= 0 mr = 24 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 1439 time to turn everything in is 1.470000 number of dielectric boundary points 77616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 22759 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) : 1.916589 object centre at (A) : 15.62400 -0.5594997 19.98150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2181456E-02 0.2408612 midg,1,midg; midg,igrid,midg 2.3951286E-02 0.3145240 1,midg,midg; igrid,midg,midg -0.4586678 0.3490295 gauss-seidel spectral radius is 0.9992743 estimated iterations to convergence 293 setup time was (sec) 1.750000 now iterating at: 14:53:08 rms-change max change #iterations 10.84327 403.8475 at 10iterations 6.341678 143.6100 at 20iterations 3.689667 66.72388 at 30iterations 2.147310 39.13226 at 40iterations 1.244114 22.74142 at 50iterations 0.7225634 12.45443 at 60iterations 0.4184282 7.080574 at 70iterations 0.2417594 4.194151 at 80iterations 0.1397619 2.207408 at 90iterations 8.1041239E-02 1.338925 at 100iterations 4.6806954E-02 0.8282471 at 110iterations 2.7063254E-02 0.4844265 at 120iterations 1.5640317E-02 0.2567101 at 130iterations 9.0511721E-03 0.1550226 at 140iterations 5.2304962E-03 8.8932037E-02 at 150iterations 3.0300345E-03 4.6941757E-02 at 160iterations 1.7588888E-03 3.1803370E-02 at 170iterations 1.0241651E-03 1.6201019E-02 at 180iterations finished qdiffx linear iterations at : 14:53:18 total time elapsed so far: 11.23000 # loops : 180 mean,max change (kT/e) : 1.0241651E-03 1.6201019E-02 energy calculations done at 11.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.40000 DelPhi exited at 14:53:18 11.400u 0.184s 0:11.92 97.1% 0+0k 0+0io 0pf+0w