Sat Oct 8 16:22:49 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 8 2011 at 16:22:49 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5834344 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): -2.260000 46.88800 ymin,ymax (A): -15.88500 29.94000 zmin,zma (A): -19.16500 41.85300 x,y,z range (A): 49.14799 45.82500 61.01800 scale (grids/A): 0.5834344 object centre (A): 22.31400 7.027501 11.34400 number of atom coordinates read : 2367 total number of charged atoms : 2288 net assigned charge : 3.900002 assigned positive charge : 354.7740 centred at (gu) : 90.05611 88.83105 88.85403 assigned negative charge : -350.8748 centred at (gu) : 90.08549 88.95776 88.88586 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5231 nv = 96 ne = 84 npr = 48099 no. pairs analyzed = 48099 no. exposed pairs = 2953 no. arc points = 20579 no. surface atoms = 1001 nbur = 1366 mkacc time = 7.9999998E-02 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 = 1.484000 m= 215 mr = 2785 m= 0 mr = 15 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.1800000 number of dielectric boundary points 2646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2047 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6799 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0011202E-09 2.3769600E-10 midg,1,midg; midg,igrid,midg 4.4019268E-09 -1.1886295E-09 1,midg,midg; igrid,midg,midg 1.4686724E-09 3.5033304E-10 gauss-seidel spectral radius is 0.9847829 estimated iterations to convergence 67 setup time was (sec) 0.3700000 now iterating at: 16:22:50 rms-change max change #iterations 8.9116693E-02 18.25146 at 10iterations 7.1774083E-03 1.279701 at 20iterations 5.9907767E-04 9.4203949E-02 at 30iterations 6.8317393E-05 1.2662172E-02 at 40iterations 1.3575917E-05 3.0458570E-03 at 50iterations finished qdiffx linear iterations at : 16:22:53 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.3575917E-05 3.0458570E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 16:22:53 3.367u 0.168s 0:03.80 92.6% 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 16:22:53 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.750303 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): -2.260000 46.88800 ymin,ymax (A): -15.88500 29.94000 zmin,zma (A): -19.16500 41.85300 x,y,z range (A): 49.14799 45.82500 61.01800 scale (grids/A): 1.750303 object centre (A): 22.31400 7.027501 11.34400 number of atom coordinates read : 2367 total number of charged atoms : 2288 net assigned charge : 3.900002 assigned positive charge : 354.7740 centred at (gu) : 90.16773 86.49271 86.56164 assigned negative charge : -350.8748 centred at (gu) : 90.25646 86.87315 86.65759 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 57848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20579 grid for indexing accessible points = 1.400000 m= 18427 mr = 39657 m= 2306 mr = 13091 m= 84 mr = 1381 m= 0 mr = 24 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 644 time to turn everything in is 0.2800000 number of dielectric boundary points 24512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 17821 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) : 0.5834344 object centre at (A) : 22.31400 7.027501 11.34400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0086050E-02 1.6293537E-02 midg,1,midg; midg,igrid,midg 1.2869298E-02 -2.0651864E-03 1,midg,midg; igrid,midg,midg 2.6254528E-03 -1.6667303E-02 gauss-seidel spectral radius is 0.9983588 estimated iterations to convergence 196 setup time was (sec) 0.4900000 now iterating at: 16:22:54 rms-change max change #iterations 3.366330 161.3770 at 10iterations 1.471695 62.37580 at 20iterations 0.6408879 26.24811 at 30iterations 0.2796752 10.69305 at 40iterations 0.1217488 4.291624 at 50iterations 5.3015716E-02 1.836222 at 60iterations 2.3083329E-02 0.8917799 at 70iterations 1.0100525E-02 0.3957968 at 80iterations 4.3969960E-03 0.1636896 at 90iterations 1.9146913E-03 6.9780827E-02 at 100iterations 8.4138365E-04 3.1065375E-02 at 110iterations 3.6837152E-04 1.3404846E-02 at 120iterations finished qdiffx linear iterations at : 16:23:01 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 3.6837152E-04 1.3404846E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 16:23:01 7.621u 0.212s 0:08.14 96.1% 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 8 2011 at 16:23:01 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.625455 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): -2.260000 46.88800 ymin,ymax (A): -15.88500 29.94000 zmin,zma (A): -19.16500 41.85300 x,y,z range (A): 49.14799 45.82500 61.01800 scale (grids/A): 2.625455 object centre (A): 22.31400 7.027501 11.34400 number of atom coordinates read : 2367 total number of charged atoms : 2288 net assigned charge : 3.900002 assigned positive charge : 354.7740 centred at (gu) : 90.25143 84.73901 84.84237 assigned negative charge : -350.8748 centred at (gu) : 90.38470 85.30970 84.98636 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 134210 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20579 grid for indexing accessible points = 1.400000 m= 62383 mr = 96680 m= 19778 mr = 50041 m= 3999 mr = 15553 m= 364 mr = 2995 m= 12 mr = 223 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 2124 time to turn everything in is 0.7100000 number of dielectric boundary points 55254 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 18290 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) : 1.750303 object centre at (A) : 22.31400 7.027501 11.34400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2363644 0.4619194 midg,1,midg; midg,igrid,midg 0.1398872 -2.9811729E-02 1,midg,midg; igrid,midg,midg 4.0072098E-02 -0.2730573 gauss-seidel spectral radius is 0.9991755 estimated iterations to convergence 275 setup time was (sec) 0.9500000 now iterating at: 16:23:02 rms-change max change #iterations 8.339311 262.6771 at 10iterations 4.715917 117.5235 at 20iterations 2.660167 59.18428 at 30iterations 1.498735 32.14282 at 40iterations 0.8392581 19.62844 at 50iterations 0.4704691 11.63820 at 60iterations 0.2632199 6.212900 at 70iterations 0.1472228 3.405733 at 80iterations 8.2172260E-02 1.743225 at 90iterations 4.5879364E-02 0.9418640 at 100iterations 2.5656553E-02 0.5482941 at 110iterations 1.4295409E-02 0.3144095 at 120iterations 7.9814019E-03 0.1839912 at 130iterations 4.4513508E-03 0.1052027 at 140iterations 2.4836133E-03 5.9055328E-02 at 150iterations 1.3927660E-03 3.1087875E-02 at 160iterations 7.7965698E-04 1.6757965E-02 at 170iterations 4.4030818E-04 1.0142088E-02 at 180iterations finished qdiffx linear iterations at : 16:23:13 total time elapsed so far: 11.95000 # loops : 180 mean,max change (kT/e) : 4.4030818E-04 1.0142088E-02 energy calculations done at 11.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.08000 DelPhi exited at 16:23:14 12.079u 0.206s 0:12.56 97.6% 0+0k 0+0io 0pf+0w