Sat Oct 8 11:33:46 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 Sat Oct 8 2011 at 11:33:46 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2379 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: 0.6698024 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): -94.86700 -46.47300 ymin,ymax (A): 54.71600 102.9660 zmin,zma (A): 76.60500 129.7550 x,y,z range (A): 48.39400 48.25000 53.15000 scale (grids/A): 0.6698024 object centre (A): -70.67000 78.84100 103.1800 number of atom coordinates read : 2379 total number of charged atoms : 2221 net assigned charge : -0.9999918 assigned positive charge : 342.5541 centred at (gu) : 88.63080 90.56879 88.22422 assigned negative charge : -343.5545 centred at (gu) : 88.67043 90.46861 88.18893 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7424 nv = 96 ne = 84 npr = 47948 no. pairs analyzed = 47948 no. exposed pairs = 3095 no. arc points = 21714 no. surface atoms = 1045 nbur = 1334 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 447 mr = 4040 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3765 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2002 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8420 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6352363E-08 3.0338434E-09 midg,1,midg; midg,igrid,midg -2.3083258E-08 2.1127876E-08 1,midg,midg; igrid,midg,midg 7.3020869E-09 -9.2689021E-09 gauss-seidel spectral radius is 0.9884337 estimated iterations to convergence 76 setup time was (sec) 0.3800000 now iterating at: 11:33:47 rms-change max change #iterations 0.1683847 27.95835 at 10iterations 1.8808577E-02 2.857740 at 20iterations 2.0527965E-03 0.3167616 at 30iterations 2.2451815E-04 2.7275085E-02 at 40iterations 2.4258336E-05 2.9487610E-03 at 50iterations finished qdiffx linear iterations at : 11:33:50 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 2.4258336E-05 2.9487610E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 11:33:50 3.480u 0.188s 0:04.23 86.5% 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 Sat Oct 8 2011 at 11:33:51 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2379 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: 2.009407 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): -94.86700 -46.47300 ymin,ymax (A): 54.71600 102.9660 zmin,zma (A): 76.60500 129.7550 x,y,z range (A): 48.39400 48.25000 53.15000 scale (grids/A): 2.009407 object centre (A): -70.67000 78.84100 103.1800 number of atom coordinates read : 2379 total number of charged atoms : 2221 net assigned charge : -0.9999918 assigned positive charge : 342.5541 centred at (gu) : 85.89178 91.70581 84.67189 assigned negative charge : -343.5545 centred at (gu) : 86.01093 91.40553 84.56654 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79372 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21714 grid for indexing accessible points = 1.400000 m= 29191 mr = 54570 m= 4958 mr = 21526 m= 314 mr = 3184 m= 8 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 817 time to turn everything in is 0.4100000 number of dielectric boundary points 34417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17597 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) : 0.6698024 object centre at (A) : -70.67000 78.84100 103.1800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5937466E-03 2.9930785E-02 midg,1,midg; midg,igrid,midg -2.4248462E-02 -6.6453363E-03 1,midg,midg; igrid,midg,midg 2.6457006E-02 -9.4958618E-03 gauss-seidel spectral radius is 0.9987491 estimated iterations to convergence 224 setup time was (sec) 0.6600000 now iterating at: 11:33:52 rms-change max change #iterations 4.361748 197.9228 at 10iterations 2.104401 67.62134 at 20iterations 1.023327 31.41708 at 30iterations 0.4919149 14.37634 at 40iterations 0.2379047 7.821629 at 50iterations 0.1153344 3.334439 at 60iterations 5.5460174E-02 1.658941 at 70iterations 2.6961120E-02 0.9060688 at 80iterations 1.3030657E-02 0.3721581 at 90iterations 6.3012037E-03 0.1943569 at 100iterations 3.0441345E-03 9.5024109E-02 at 110iterations 1.4707212E-03 4.3721199E-02 at 120iterations finished qdiffx linear iterations at : 11:34:00 total time elapsed so far: 8.650000 # loops : 120 mean,max change (kT/e) : 1.4707212E-03 4.3721199E-02 energy calculations done at 8.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.780000 DelPhi exited at 11:34:00 8.787u 0.318s 0:09.39 96.8% 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 Sat Oct 8 2011 at 11:34:00 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2379 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: 3.014111 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): -94.86700 -46.47300 ymin,ymax (A): 54.71600 102.9660 zmin,zma (A): 76.60500 129.7550 x,y,z range (A): 48.39400 48.25000 53.15000 scale (grids/A): 3.014111 object centre (A): -70.67000 78.84100 103.1800 number of atom coordinates read : 2379 total number of charged atoms : 2221 net assigned charge : -0.9999918 assigned positive charge : 342.5541 centred at (gu) : 83.83756 92.55862 82.00777 assigned negative charge : -343.5545 centred at (gu) : 84.01630 92.10821 81.84975 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 183777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21714 grid for indexing accessible points = 1.400000 m= 92348 mr = 132293 m= 35108 mr = 75537 m= 9194 mr = 28341 m= 1485 mr = 7044 m= 90 mr = 1064 m= 0 mr = 42 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 2743 time to turn everything in is 1.070000 number of dielectric boundary points 77681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 17768 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) : 2.009407 object centre at (A) : -70.67000 78.84100 103.1800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4422379E-03 0.2546437 midg,1,midg; midg,igrid,midg -0.2206436 -6.5044142E-02 1,midg,midg; igrid,midg,midg 0.2726223 -0.1327407 gauss-seidel spectral radius is 0.9992913 estimated iterations to convergence 296 setup time was (sec) 1.350000 now iterating at: 11:34:02 rms-change max change #iterations 10.15858 413.8373 at 10iterations 6.022887 147.4297 at 20iterations 3.554742 84.36057 at 30iterations 2.088693 40.06610 at 40iterations 1.225268 27.78852 at 50iterations 0.7179554 13.94061 at 60iterations 0.4201015 7.284773 at 70iterations 0.2453433 4.762356 at 80iterations 0.1433057 2.786760 at 90iterations 8.3498284E-02 1.534786 at 100iterations 4.8714787E-02 0.9212494 at 110iterations 2.8399557E-02 0.4596519 at 120iterations 1.6549110E-02 0.3081160 at 130iterations 9.6151801E-03 0.1768770 at 140iterations 5.6134658E-03 0.1022873 at 150iterations 3.2653254E-03 6.0821533E-02 at 160iterations 1.9015230E-03 3.3353806E-02 at 170iterations 1.1090830E-03 1.9883633E-02 at 180iterations finished qdiffx linear iterations at : 11:34:16 total time elapsed so far: 15.29000 # loops : 180 mean,max change (kT/e) : 1.1090830E-03 1.9883633E-02 energy calculations done at 15.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.42000 DelPhi exited at 11:34:16 15.420u 0.333s 0:16.11 97.7% 0+0k 0+0io 0pf+0w