Sat Oct 15 11:28:38 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 15 2011 at 11:28:38 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3347 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: 0.5424927 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): -11.47200 41.84300 ymin,ymax (A): -38.50200 27.12100 zmin,zma (A): -15.98900 34.14600 x,y,z range (A): 53.31500 65.62300 50.13500 scale (grids/A): 0.5424927 object centre (A): 15.18550 -5.690501 9.078501 number of atom coordinates read : 3347 total number of charged atoms : 3204 net assigned charge : -0.4999925 assigned positive charge : 501.9806 centred at (gu) : 90.16573 91.68770 90.61174 assigned negative charge : -502.4819 centred at (gu) : 90.15442 91.63470 90.56944 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6437 nv = 96 ne = 84 npr = 67346 no. pairs analyzed = 67346 no. exposed pairs = 4078 no. arc points = 28119 no. surface atoms = 1378 nbur = 1969 mkacc time = 0.1100000 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 = 1.568000 m= 281 mr = 3509 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2960 ## 418 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8496 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6998362E-10 2.8144626E-10 midg,1,midg; midg,igrid,midg -2.5310146E-10 4.7844684E-10 1,midg,midg; igrid,midg,midg -1.0548125E-10 4.0260979E-11 gauss-seidel spectral radius is 0.9825093 estimated iterations to convergence 62 setup time was (sec) 0.4700000 now iterating at: 11:28:39 rms-change max change #iterations 7.6031484E-02 11.09953 at 10iterations 5.0973939E-03 0.7541103 at 20iterations 3.8464641E-04 6.6625595E-02 at 30iterations 4.8064176E-05 1.0699272E-02 at 40iterations 9.9787521E-06 2.6140213E-03 at 50iterations finished qdiffx linear iterations at : 11:28:43 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 9.9787521E-06 2.6140213E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 11:28:43 4.032u 0.286s 0:05.64 76.4% 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 Sat Oct 15 2011 at 11:28:43 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3347 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: 1.627478 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): -11.47200 41.84300 ymin,ymax (A): -38.50200 27.12100 zmin,zma (A): -15.98900 34.14600 x,y,z range (A): 53.31500 65.62300 50.13500 scale (grids/A): 1.627478 object centre (A): 15.18550 -5.690501 9.078501 number of atom coordinates read : 3347 total number of charged atoms : 3204 net assigned charge : -0.4999925 assigned positive charge : 501.9806 centred at (gu) : 90.49626 95.06223 91.83458 assigned negative charge : -502.4819 centred at (gu) : 90.46301 94.90362 91.70782 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 71938 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28119 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23546 mr = 50530 m= 2402 mr = 16645 m= 75 mr = 1158 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 393 time to turn everything in is 0.3800000 number of dielectric boundary points 29624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 402 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 24583 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) : 0.5424927 object centre at (A) : 15.18550 -5.690501 9.078501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5495858E-03 3.9536245E-03 midg,1,midg; midg,igrid,midg 6.6536446E-03 1.5198971E-02 1,midg,midg; igrid,midg,midg 1.4390319E-03 -1.0884942E-03 gauss-seidel spectral radius is 0.9982039 estimated iterations to convergence 187 setup time was (sec) 0.6500000 now iterating at: 11:28:44 rms-change max change #iterations 3.537367 146.1454 at 10iterations 1.481286 54.44478 at 20iterations 0.6219652 22.14006 at 30iterations 0.2607543 8.105217 at 40iterations 0.1093685 3.918352 at 50iterations 4.5997169E-02 1.851059 at 60iterations 1.9314697E-02 0.6642723 at 70iterations 8.1217904E-03 0.2791653 at 80iterations 3.4177720E-03 0.1128502 at 90iterations 1.4403061E-03 4.8778534E-02 at 100iterations 6.0813501E-04 2.1783352E-02 at 110iterations 2.6268605E-04 8.7909698E-03 at 120iterations finished qdiffx linear iterations at : 11:28:53 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 2.6268605E-04 8.7909698E-03 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.440000 DelPhi exited at 11:28:54 9.446u 0.299s 0:10.02 97.1% 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 15 2011 at 11:28:54 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3347 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: 2.441217 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): -11.47200 41.84300 ymin,ymax (A): -38.50200 27.12100 zmin,zma (A): -15.98900 34.14600 x,y,z range (A): 53.31500 65.62300 50.13500 scale (grids/A): 2.441217 object centre (A): 15.18550 -5.690501 9.078501 number of atom coordinates read : 3347 total number of charged atoms : 3204 net assigned charge : -0.4999925 assigned positive charge : 501.9806 centred at (gu) : 90.74422 97.59309 92.75163 assigned negative charge : -502.4819 centred at (gu) : 90.69460 97.35528 92.56165 start vw surface at 0.1100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 167100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28119 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 81223 mr = 123062 m= 23807 mr = 65548 m= 3734 mr = 18109 m= 254 mr = 2359 m= 8 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 1493 time to turn everything in is 0.9400000 number of dielectric boundary points 66942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 25605 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) : 1.627478 object centre at (A) : 15.18550 -5.690501 9.078501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1325923 7.5364091E-02 midg,1,midg; midg,igrid,midg 0.1210898 0.4572105 1,midg,midg; igrid,midg,midg 4.6174504E-02 -3.6761230E-03 gauss-seidel spectral radius is 0.9991493 estimated iterations to convergence 271 setup time was (sec) 1.260000 now iterating at: 11:28:55 rms-change max change #iterations 9.128371 314.3835 at 10iterations 5.149233 127.1523 at 20iterations 2.901956 62.49264 at 30iterations 1.621472 36.07470 at 40iterations 0.9042905 19.37385 at 50iterations 0.5026520 10.53737 at 60iterations 0.2798752 5.747983 at 70iterations 0.1553331 3.304291 at 80iterations 8.5877046E-02 1.968424 at 90iterations 4.7535606E-02 0.9879990 at 100iterations 2.6366917E-02 0.5300822 at 110iterations 1.4592434E-02 0.2858219 at 120iterations 8.0769891E-03 0.1577253 at 130iterations 4.4716462E-03 9.5893860E-02 at 140iterations 2.4758242E-03 5.1200867E-02 at 150iterations 1.3740681E-03 2.5329590E-02 at 160iterations 7.6816819E-04 1.5129089E-02 at 170iterations 4.3192349E-04 8.4234476E-03 at 180iterations finished qdiffx linear iterations at : 11:29:09 total time elapsed so far: 14.92000 # loops : 180 mean,max change (kT/e) : 4.3192349E-04 8.4234476E-03 energy calculations done at 14.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.07000 DelPhi exited at 11:29:10 15.067u 0.357s 0:16.44 93.7% 0+0k 0+0io 0pf+0w