Tue Oct 11 06:00:48 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 Tue Oct 11 2011 at 06:00:48 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 0.7071068 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): 25.70300 72.08200 ymin,ymax (A): -18.73200 31.61400 zmin,zma (A): 3.943000 46.19400 x,y,z range (A): 46.37900 50.34600 42.25100 scale (grids/A): 0.7071068 object centre (A): 48.89250 6.441000 25.06850 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 89.20573 90.17297 90.34305 assigned negative charge : -317.2741 centred at (gu) : 89.33806 90.12307 90.42661 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7158 nv = 96 ne = 84 npr = 42424 no. pairs analyzed = 42424 no. exposed pairs = 2600 no. arc points = 17585 no. surface atoms = 890 nbur = 1428 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 486 mr = 4166 m= 1 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1595 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7940 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9239784E-08 1.2540791E-08 midg,1,midg; midg,igrid,midg 2.8077933E-08 8.1420957E-08 1,midg,midg; igrid,midg,midg 1.3915080E-07 -1.0600883E-08 gauss-seidel spectral radius is 0.9895772 estimated iterations to convergence 80 setup time was (sec) 0.3700000 now iterating at: 06:00:49 rms-change max change #iterations 0.2010247 30.44488 at 10iterations 2.5319323E-02 3.327118 at 20iterations 3.3039963E-03 0.4241638 at 30iterations 5.5934238E-04 7.3772430E-02 at 40iterations 1.4589263E-04 1.7068863E-02 at 50iterations finished qdiffx linear iterations at : 06:00:52 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.4589263E-04 1.7068863E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 06:00:52 3.504u 0.202s 0:04.43 83.5% 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 Tue Oct 11 2011 at 06:00:52 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 2.121320 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): 25.70300 72.08200 ymin,ymax (A): -18.73200 31.61400 zmin,zma (A): 3.943000 46.19400 x,y,z range (A): 46.37900 50.34600 42.25100 scale (grids/A): 2.121320 object centre (A): 48.89250 6.441000 25.06850 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 87.61732 90.51871 91.02940 assigned negative charge : -317.2741 centred at (gu) : 88.01414 90.36918 91.27986 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76046 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17585 grid for indexing accessible points = 1.400000 m= 31050 mr = 54191 m= 5967 mr = 23682 m= 537 mr = 4050 m= 21 mr = 277 m= 0 mr = 9 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 31412 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15806 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) : 0.7071068 object centre at (A) : 48.89250 6.441000 25.06850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0255992E-02 2.8664364E-02 midg,1,midg; midg,igrid,midg 4.7015175E-02 2.6638255E-02 1,midg,midg; igrid,midg,midg 4.5715876E-02 -4.8351537E-02 gauss-seidel spectral radius is 0.9988323 estimated iterations to convergence 232 setup time was (sec) 0.6200000 now iterating at: 06:00:53 rms-change max change #iterations 4.636102 228.3676 at 10iterations 2.292289 77.70399 at 20iterations 1.139283 37.19025 at 30iterations 0.5655012 16.34973 at 40iterations 0.2807286 8.953674 at 50iterations 0.1392460 4.087499 at 60iterations 6.9320627E-02 2.047340 at 70iterations 3.4517426E-02 1.090600 at 80iterations 1.7230421E-02 0.5074501 at 90iterations 8.6295176E-03 0.2555170 at 100iterations 4.3374817E-03 0.1311598 at 110iterations 2.2211927E-03 6.2774658E-02 at 120iterations finished qdiffx linear iterations at : 06:01:01 total time elapsed so far: 8.110000 # loops : 120 mean,max change (kT/e) : 2.2211927E-03 6.2774658E-02 energy calculations done at 8.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 06:01:01 8.245u 0.235s 0:09.02 93.9% 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 Tue Oct 11 2011 at 06:01:02 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.181981 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): 25.70300 72.08200 ymin,ymax (A): -18.73200 31.61400 zmin,zma (A): 3.943000 46.19400 x,y,z range (A): 46.37900 50.34600 42.25100 scale (grids/A): 3.181981 object centre (A): 48.89250 6.441000 25.06850 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 86.42600 90.77803 91.54401 assigned negative charge : -317.2741 centred at (gu) : 87.02139 90.55367 91.91980 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 175031 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17585 grid for indexing accessible points = 1.400000 m= 96302 mr = 130320 m= 39466 mr = 80336 m= 11280 mr = 32620 m= 2186 mr = 8823 m= 322 mr = 1624 m= 17 mr = 213 m= 0 mr = 6 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 70662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 15952 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) : 2.121320 object centre at (A) : 48.89250 6.441000 25.06850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1257398 0.2451547 midg,1,midg; midg,igrid,midg 0.3681077 0.1163131 1,midg,midg; igrid,midg,midg 0.4419697 -0.5971116 gauss-seidel spectral radius is 0.9992977 estimated iterations to convergence 298 setup time was (sec) 1.440000 now iterating at: 06:01:03 rms-change max change #iterations 10.37595 346.7543 at 10iterations 6.154497 137.4630 at 20iterations 3.648056 85.91045 at 30iterations 2.154923 54.32561 at 40iterations 1.271069 24.82703 at 50iterations 0.7488331 14.71801 at 60iterations 0.4398569 8.357853 at 70iterations 0.2588614 5.018236 at 80iterations 0.1519292 3.287335 at 90iterations 8.9069463E-02 1.798100 at 100iterations 5.2436244E-02 0.8959038 at 110iterations 3.0890269E-02 0.5589619 at 120iterations 1.8302860E-02 0.3280182 at 130iterations 1.0941109E-02 0.1971879 at 140iterations 6.6650785E-03 0.1294441 at 150iterations 4.1682459E-03 7.7545166E-02 at 160iterations 2.7311505E-03 6.3137054E-02 at 170iterations 1.8929313E-03 3.6304474E-02 at 180iterations finished qdiffx linear iterations at : 06:01:15 total time elapsed so far: 13.56000 # loops : 180 mean,max change (kT/e) : 1.8929313E-03 3.6304474E-02 energy calculations done at 13.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.69000 DelPhi exited at 06:01:16 13.696u 0.253s 0:14.67 95.0% 0+0k 0+0io 0pf+0w