Sun Oct 9 00:15:53 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 Sun Oct 9 2011 at 00:15:53 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 = 3390 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5543530 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): -48.10000 8.063000 ymin,ymax (A): 175.1130 239.3320 zmin,zma (A): 78.26000 141.9110 x,y,z range (A): 56.16300 64.21901 63.65101 scale (grids/A): 0.5543530 object centre (A): -20.01850 207.2225 110.0855 number of atom coordinates read : 3390 total number of charged atoms : 3246 net assigned charge : 14.50002 assigned positive charge : 502.0544 centred at (gu) : 89.51333 90.24732 90.70960 assigned negative charge : -487.5562 centred at (gu) : 89.35892 90.25593 90.81301 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7111 nv = 96 ne = 84 npr = 64698 no. pairs analyzed = 64698 no. exposed pairs = 4615 no. arc points = 33722 no. surface atoms = 1522 nbur = 1868 mkacc time = 0.1400000 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 = 1.540000 m= 310 mr = 3500 m= 3 mr = 12 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 0.3600000 number of dielectric boundary points 3912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3390 ## 439 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9139 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9197304E-09 2.5781885E-10 midg,1,midg; midg,igrid,midg 1.2735394E-09 1.2508510E-09 1,midg,midg; igrid,midg,midg -3.4195813E-10 2.4595443E-09 gauss-seidel spectral radius is 0.9832667 estimated iterations to convergence 64 setup time was (sec) 0.5800000 now iterating at: 00:15:54 rms-change max change #iterations 8.4795982E-02 13.05029 at 10iterations 5.8381730E-03 0.9285393 at 20iterations 4.1385862E-04 6.4079285E-02 at 30iterations 3.4271012E-05 5.6037903E-03 at 40iterations 4.3049854E-06 4.8112869E-04 at 50iterations finished qdiffx linear iterations at : 00:15:57 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 4.3049854E-06 4.8112869E-04 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 00:15:57 3.301u 0.174s 0:03.82 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 Sun Oct 9 2011 at 00:15:57 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 = 3390 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: 1.663059 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): -48.10000 8.063000 ymin,ymax (A): 175.1130 239.3320 zmin,zma (A): 78.26000 141.9110 x,y,z range (A): 56.16300 64.21901 63.65101 scale (grids/A): 1.663059 object centre (A): -20.01850 207.2225 110.0855 number of atom coordinates read : 3390 total number of charged atoms : 3246 net assigned charge : 14.50002 assigned positive charge : 502.0544 centred at (gu) : 88.53907 90.74094 92.12785 assigned negative charge : -487.5562 centred at (gu) : 88.07646 90.76749 92.43867 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78560 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33722 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24956 mr = 51772 m= 2901 mr = 16982 m= 77 mr = 1391 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.5300000 number of dielectric boundary points 36347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 393 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 24935 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) : 0.5543530 object centre at (A) : -20.01850 207.2225 110.0855 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7047031E-03 -1.4936807E-02 midg,1,midg; midg,igrid,midg 2.7545080E-02 2.8029006E-02 1,midg,midg; igrid,midg,midg -1.1685742E-02 2.1091850E-02 gauss-seidel spectral radius is 0.9983191 estimated iterations to convergence 194 setup time was (sec) 0.7900000 now iterating at: 00:15:58 rms-change max change #iterations 3.660516 204.2814 at 10iterations 1.563102 71.05203 at 20iterations 0.6711810 22.98900 at 30iterations 0.2882381 9.848053 at 40iterations 0.1240378 4.065514 at 50iterations 5.3100940E-02 1.706347 at 60iterations 2.2922672E-02 0.8247414 at 70iterations 9.8925233E-03 0.3220248 at 80iterations 4.2342423E-03 0.1305113 at 90iterations 1.8328418E-03 6.4018250E-02 at 100iterations 7.9070125E-04 2.5150299E-02 at 110iterations 3.4047972E-04 1.1306763E-02 at 120iterations finished qdiffx linear iterations at : 00:16:04 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 3.4047972E-04 1.1306763E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 00:16:05 7.058u 0.177s 0:07.54 95.7% 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 Sun Oct 9 2011 at 00:16:05 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 = 3390 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: 2.494588 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): -48.10000 8.063000 ymin,ymax (A): 175.1130 239.3320 zmin,zma (A): 78.26000 141.9110 x,y,z range (A): 56.16300 64.21901 63.65101 scale (grids/A): 2.494588 object centre (A): -20.01850 207.2225 110.0855 number of atom coordinates read : 3390 total number of charged atoms : 3246 net assigned charge : 14.50002 assigned positive charge : 502.0544 centred at (gu) : 87.80862 91.11116 93.19153 assigned negative charge : -487.5562 centred at (gu) : 87.11468 91.15115 93.65817 start vw surface at 0.1800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 182071 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33722 grid for indexing accessible points = 1.400000 m= 84385 mr = 126918 m= 25738 mr = 65953 m= 4630 mr = 19194 m= 336 mr = 2980 m= 6 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 120 time to turn everything in is 1.300000 number of dielectric boundary points 82003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 25946 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) : 1.663059 object centre at (A) : -20.01850 207.2225 110.0855 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2220719 -0.1539063 midg,1,midg; midg,igrid,midg 0.2661259 0.5077887 1,midg,midg; igrid,midg,midg -0.2782446 0.2560403 gauss-seidel spectral radius is 0.9992024 estimated iterations to convergence 280 setup time was (sec) 1.590000 now iterating at: 00:16:07 rms-change max change #iterations 9.473587 357.2334 at 10iterations 5.511286 131.1519 at 20iterations 3.177410 73.30048 at 30iterations 1.823599 39.59687 at 40iterations 1.039505 21.84340 at 50iterations 0.5917238 11.71408 at 60iterations 0.3357154 6.839809 at 70iterations 0.1900473 3.743421 at 80iterations 0.1074255 2.059670 at 90iterations 6.0665764E-02 1.275787 at 100iterations 3.4204397E-02 0.6795268 at 110iterations 1.9324651E-02 0.3904510 at 120iterations 1.0865763E-02 0.2161698 at 130iterations 6.1145960E-03 0.1176062 at 140iterations 3.4450279E-03 6.6677094E-02 at 150iterations 1.9359706E-03 3.7506580E-02 at 160iterations 1.0918693E-03 2.0124912E-02 at 170iterations 6.1486877E-04 1.1756897E-02 at 180iterations finished qdiffx linear iterations at : 00:16:16 total time elapsed so far: 11.35000 # loops : 180 mean,max change (kT/e) : 6.1486877E-04 1.1756897E-02 energy calculations done at 11.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.51000 DelPhi exited at 00:16:17 11.517u 0.179s 0:12.01 97.2% 0+0k 0+0io 0pf+0w