Mon Oct 10 20:16:53 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 20:16:54 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2615 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: 0.6172412 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): -10.92700 41.88600 ymin,ymax (A): 28.50900 82.55800 zmin,zma (A): -12.90600 44.77000 x,y,z range (A): 52.81300 54.04900 57.67599 scale (grids/A): 0.6172412 object centre (A): 15.47950 55.53350 15.93200 number of atom coordinates read : 2615 total number of charged atoms : 2478 net assigned charge : -3.499990 assigned positive charge : 389.2277 centred at (gu) : 89.25378 90.85135 90.77034 assigned negative charge : -392.7288 centred at (gu) : 89.31179 90.95388 90.76836 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6688 nv = 96 ne = 84 npr = 52814 no. pairs analyzed = 52814 no. exposed pairs = 3571 no. arc points = 25931 no. surface atoms = 1186 nbur = 1429 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 332 mr = 3308 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2469 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8083 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2686881E-09 -2.8636642E-09 midg,1,midg; midg,igrid,midg 3.0601799E-09 -1.0858924E-08 1,midg,midg; igrid,midg,midg 1.2350601E-09 -5.2369828E-09 gauss-seidel spectral radius is 0.9864202 estimated iterations to convergence 70 setup time was (sec) 0.5600000 now iterating at: 20:16:54 rms-change max change #iterations 0.1208562 17.56254 at 10iterations 1.1099984E-02 1.729622 at 20iterations 1.0669556E-03 0.1659641 at 30iterations 1.4792422E-04 2.7399063E-02 at 40iterations 3.7889724E-05 8.0451965E-03 at 50iterations finished qdiffx linear iterations at : 20:16:57 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 3.7889724E-05 8.0451965E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 20:16:58 3.365u 0.160s 0:04.29 82.0% 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 20:16:58 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2615 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: 1.851724 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): -10.92700 41.88600 ymin,ymax (A): 28.50900 82.55800 zmin,zma (A): -12.90600 44.77000 x,y,z range (A): 52.81300 54.04900 57.67599 scale (grids/A): 1.851724 object centre (A): 15.47950 55.53350 15.93200 number of atom coordinates read : 2615 total number of charged atoms : 2478 net assigned charge : -3.499990 assigned positive charge : 389.2277 centred at (gu) : 87.76089 92.55328 92.31047 assigned negative charge : -392.7288 centred at (gu) : 87.93531 92.86165 92.30521 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 71659 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25931 grid for indexing accessible points = 1.400000 m= 23870 mr = 46672 m= 3598 mr = 16559 m= 162 mr = 2005 m= 2 mr = 34 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 34021 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19409 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) : 0.6172412 object centre at (A) : 15.47950 55.53350 15.93200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3183792E-03 -4.2139798E-02 midg,1,midg; midg,igrid,midg 1.0341866E-02 -2.8348291E-02 1,midg,midg; igrid,midg,midg 2.3771659E-02 -8.0157752E-04 gauss-seidel spectral radius is 0.9985779 estimated iterations to convergence 210 setup time was (sec) 0.8400000 now iterating at: 20:16:59 rms-change max change #iterations 4.084491 208.4318 at 10iterations 1.873822 72.59286 at 20iterations 0.8661131 28.71764 at 30iterations 0.3985588 13.87686 at 40iterations 0.1830865 5.959675 at 50iterations 8.4574714E-02 2.850594 at 60iterations 3.8898408E-02 1.280746 at 70iterations 1.7890202E-02 0.6807032 at 80iterations 8.2620792E-03 0.2996273 at 90iterations 3.8120642E-03 0.1230993 at 100iterations 1.7724299E-03 6.3588142E-02 at 110iterations 8.2083844E-04 2.7269363E-02 at 120iterations finished qdiffx linear iterations at : 20:17:05 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 8.2083844E-04 2.7269363E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 20:17:06 7.460u 0.161s 0:08.39 90.8% 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 20:17:06 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2615 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: 2.777585 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): -10.92700 41.88600 ymin,ymax (A): 28.50900 82.55800 zmin,zma (A): -12.90600 44.77000 x,y,z range (A): 52.81300 54.04900 57.67599 scale (grids/A): 2.777585 object centre (A): 15.47950 55.53350 15.93200 number of atom coordinates read : 2615 total number of charged atoms : 2478 net assigned charge : -3.499990 assigned positive charge : 389.2277 centred at (gu) : 86.64120 93.82964 93.46568 assigned negative charge : -392.7288 centred at (gu) : 86.90290 94.29239 93.45775 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 166086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25931 grid for indexing accessible points = 1.400000 m= 77903 mr = 114608 m= 26936 mr = 60878 m= 6155 mr = 20880 m= 747 mr = 4252 m= 32 mr = 422 m= 0 mr = 9 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 76810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 19823 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) : 1.851724 object centre at (A) : 15.47950 55.53350 15.93200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3917634E-02 -0.4900421 midg,1,midg; midg,igrid,midg 0.1467174 -0.1733433 1,midg,midg; igrid,midg,midg 0.2314710 -5.2438639E-02 gauss-seidel spectral radius is 0.9992555 estimated iterations to convergence 289 setup time was (sec) 1.670000 now iterating at: 20:17:08 rms-change max change #iterations 9.821388 375.3635 at 10iterations 5.808210 143.8741 at 20iterations 3.403392 75.50217 at 30iterations 1.980213 48.86296 at 40iterations 1.149663 22.83136 at 50iterations 0.6649721 14.15613 at 60iterations 0.3839339 7.994221 at 70iterations 0.2215565 4.138450 at 80iterations 0.1279679 2.441128 at 90iterations 7.3421456E-02 1.341961 at 100iterations 4.2173564E-02 0.8030300 at 110iterations 2.4237245E-02 0.4489231 at 120iterations 1.3928924E-02 0.2652397 at 130iterations 8.0257775E-03 0.1464844 at 140iterations 4.6200212E-03 8.4194183E-02 at 150iterations 2.6611516E-03 4.8721313E-02 at 160iterations 1.5359295E-03 2.9642105E-02 at 170iterations 8.9219783E-04 1.9792557E-02 at 180iterations finished qdiffx linear iterations at : 20:17:18 total time elapsed so far: 11.79000 # loops : 180 mean,max change (kT/e) : 8.9219783E-04 1.9792557E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 20:17:19 11.975u 0.190s 0:12.77 95.2% 0+0k 0+0io 0pf+0w