Mon Oct 10 16:57:09 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 Mon Oct 10 2011 at 16:57:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2278 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: 0.6751887 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): -3.048000 49.67800 ymin,ymax (A): -1.818000 44.94700 zmin,zma (A): -4.413000 41.66500 x,y,z range (A): 52.72600 46.76500 46.07800 scale (grids/A): 0.6751887 object centre (A): 23.31500 21.56450 18.62600 number of atom coordinates read : 2278 total number of charged atoms : 2202 net assigned charge : -1.999997 assigned positive charge : 335.8053 centred at (gu) : 89.36405 88.91360 89.88098 assigned negative charge : -337.8059 centred at (gu) : 89.41427 88.82721 89.91486 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7176 nv = 96 ne = 84 npr = 45962 no. pairs analyzed = 45962 no. exposed pairs = 3027 no. arc points = 21030 no. surface atoms = 1018 nbur = 1260 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 466 mr = 3887 m= 8 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2800000 number of dielectric boundary points 3684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1929 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8392 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1201545E-09 -1.5587309E-08 midg,1,midg; midg,igrid,midg -3.6730405E-08 1.1211634E-08 1,midg,midg; igrid,midg,midg 5.9546776E-09 -1.7677788E-08 gauss-seidel spectral radius is 0.9886043 estimated iterations to convergence 76 setup time was (sec) 0.5800000 now iterating at: 16:57:54 rms-change max change #iterations 0.1691589 25.29952 at 10iterations 1.9298267E-02 2.708785 at 20iterations 2.1135246E-03 0.3226261 at 30iterations 3.0375735E-04 4.3670654E-02 at 40iterations 6.9879279E-05 9.2773438E-03 at 50iterations finished qdiffx linear iterations at : 16:57:59 total time elapsed so far: 5.500000 # loops : 50 mean,max change (kT/e) : 6.9879279E-05 9.2773438E-03 energy calculations done at 5.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.680000 DelPhi exited at 16:57:59 5.682u 0.516s 0:50.73 12.2% 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 Mon Oct 10 2011 at 16:58:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2278 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: 2.025566 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): -3.048000 49.67800 ymin,ymax (A): -1.818000 44.94700 zmin,zma (A): -4.413000 41.66500 x,y,z range (A): 52.72600 46.76500 46.07800 scale (grids/A): 2.025566 object centre (A): 23.31500 21.56450 18.62600 number of atom coordinates read : 2278 total number of charged atoms : 2202 net assigned charge : -1.999997 assigned positive charge : 335.8053 centred at (gu) : 88.09164 86.74071 89.64272 assigned negative charge : -337.8059 centred at (gu) : 88.24267 86.48167 89.74458 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 76044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21030 grid for indexing accessible points = 1.400000 m= 29071 mr = 52233 m= 5608 mr = 21289 m= 492 mr = 3603 m= 13 mr = 241 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1118 time to turn everything in is 0.6400000 number of dielectric boundary points 33862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17446 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) : 0.6751887 object centre at (A) : 23.31500 21.56450 18.62600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4640399E-03 -2.9786889E-02 midg,1,midg; midg,igrid,midg -4.3640599E-02 1.5607329E-02 1,midg,midg; igrid,midg,midg 6.4015046E-02 9.0917302E-03 gauss-seidel spectral radius is 0.9987645 estimated iterations to convergence 225 setup time was (sec) 0.9900000 now iterating at: 16:58:05 rms-change max change #iterations 4.410467 208.3009 at 10iterations 2.138420 63.34705 at 20iterations 1.046674 35.34890 at 30iterations 0.5071248 14.94338 at 40iterations 0.2469147 7.650970 at 50iterations 0.1204105 4.048981 at 60iterations 5.8313202E-02 1.766551 at 70iterations 2.8513851E-02 0.9386463 at 80iterations 1.3969260E-02 0.4366169 at 90iterations 6.7926054E-03 0.1943626 at 100iterations 3.3115395E-03 9.6046448E-02 at 110iterations 1.6289685E-03 5.4018021E-02 at 120iterations finished qdiffx linear iterations at : 16:58:16 total time elapsed so far: 12.37000 # loops : 120 mean,max change (kT/e) : 1.6289685E-03 5.4018021E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.52000 DelPhi exited at 16:58:17 12.528u 0.562s 0:16.79 77.9% 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 Mon Oct 10 2011 at 16:58:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2278 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: 3.038349 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): -3.048000 49.67800 ymin,ymax (A): -1.818000 44.94700 zmin,zma (A): -4.413000 41.66500 x,y,z range (A): 52.72600 46.76500 46.07800 scale (grids/A): 3.038349 object centre (A): 23.31500 21.56450 18.62600 number of atom coordinates read : 2278 total number of charged atoms : 2202 net assigned charge : -1.999997 assigned positive charge : 335.8053 centred at (gu) : 87.13733 85.11100 89.46392 assigned negative charge : -337.8059 centred at (gu) : 87.36402 84.72243 89.61688 start vw surface at 0.1100000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 175501 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21030 grid for indexing accessible points = 1.400000 m= 90303 mr = 126575 m= 36517 mr = 73431 m= 10528 mr = 29324 m= 2038 mr = 7952 m= 212 mr = 1365 m= 13 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 3794 time to turn everything in is 1.750000 number of dielectric boundary points 76340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 17612 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) : 2.025566 object centre at (A) : 23.31500 21.56450 18.62600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1264144E-03 -0.2554182 midg,1,midg; midg,igrid,midg -0.3300166 0.3019097 1,midg,midg; igrid,midg,midg 0.7340919 0.1635602 gauss-seidel spectral radius is 0.9992950 estimated iterations to convergence 297 setup time was (sec) 2.130000 now iterating at: 16:58:19 rms-change max change #iterations 10.14867 411.3258 at 10iterations 5.995756 126.5418 at 20iterations 3.552657 75.94522 at 30iterations 2.084380 36.96769 at 40iterations 1.230572 28.20484 at 50iterations 0.7217484 14.02016 at 60iterations 0.4237204 8.348042 at 70iterations 0.2483685 4.373100 at 80iterations 0.1449936 2.557102 at 90iterations 8.4661499E-02 1.643555 at 100iterations 4.9660519E-02 0.8833027 at 110iterations 2.8923761E-02 0.5140610 at 120iterations 1.6936570E-02 0.3076744 at 130iterations 9.8734116E-03 0.1751583 at 140iterations 5.7839449E-03 0.1000376 at 150iterations 3.3959323E-03 5.8322906E-02 at 160iterations 2.0070020E-03 3.4322500E-02 at 170iterations 1.2013325E-03 2.1301270E-02 at 180iterations finished qdiffx linear iterations at : 16:58:39 total time elapsed so far: 21.79000 # loops : 180 mean,max change (kT/e) : 1.2013325E-03 2.1301270E-02 energy calculations done at 21.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.96000 DelPhi exited at 16:58:40 21.962u 0.550s 0:22.83 98.5% 0+0k 0+0io 0pf+0w