Sat Oct 8 11:49:09 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 11:49:09 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 = 2587 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5682544 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): -14.41700 35.89400 ymin,ymax (A): 30.82600 74.91700 zmin,zma (A): -11.18100 51.46700 x,y,z range (A): 50.31100 44.09100 62.64800 scale (grids/A): 0.5682544 object centre (A): 10.73850 52.87150 20.14300 number of atom coordinates read : 2587 total number of charged atoms : 2438 net assigned charge : -2.999990 assigned positive charge : 377.8216 centred at (gu) : 91.19164 90.78741 90.71654 assigned negative charge : -380.8224 centred at (gu) : 91.15771 90.78995 90.74303 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5466 nv = 96 ne = 84 npr = 52503 no. pairs analyzed = 52503 no. exposed pairs = 3328 no. arc points = 23571 no. surface atoms = 1126 nbur = 1461 mkacc time = 0.1300000 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 = 1.512000 m= 225 mr = 2787 m= 0 mr = 8 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2428 ## 301 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7048 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6998658E-11 -9.1246294E-10 midg,1,midg; midg,igrid,midg -3.3528094E-10 -5.5972466E-10 1,midg,midg; igrid,midg,midg -6.5315992E-10 -4.2967650E-13 gauss-seidel spectral radius is 0.9839925 estimated iterations to convergence 65 setup time was (sec) 0.5600000 now iterating at: 11:49:10 rms-change max change #iterations 7.9790264E-02 12.99420 at 10iterations 5.9725535E-03 1.002872 at 20iterations 4.4878811E-04 7.4241638E-02 at 30iterations 3.3395288E-05 5.4302216E-03 at 40iterations 2.5859079E-06 4.1151047E-04 at 50iterations finished qdiffx linear iterations at : 11:49:14 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 2.5859079E-06 4.1151047E-04 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.660000 DelPhi exited at 11:49:15 4.667u 0.398s 0:05.36 94.2% 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 11:49:15 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 = 2587 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.704763 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): -14.41700 35.89400 ymin,ymax (A): 30.82600 74.91700 zmin,zma (A): -11.18100 51.46700 x,y,z range (A): 50.31100 44.09100 62.64800 scale (grids/A): 1.704763 object centre (A): 10.73850 52.87150 20.14300 number of atom coordinates read : 2587 total number of charged atoms : 2438 net assigned charge : -2.999990 assigned positive charge : 377.8216 centred at (gu) : 93.57443 92.36172 92.14903 assigned negative charge : -380.8224 centred at (gu) : 93.47308 92.36955 92.22867 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 60115 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23571 grid for indexing accessible points = 1.400000 m= 18542 mr = 40185 m= 1828 mr = 12644 m= 42 mr = 896 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 26798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 18848 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) : 0.5682544 object centre at (A) : 10.73850 52.87150 20.14300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6883204E-03 -1.9371141E-02 midg,1,midg; midg,igrid,midg 1.6653957E-03 -4.4616838E-03 1,midg,midg; igrid,midg,midg -5.5661169E-03 1.1714650E-03 gauss-seidel spectral radius is 0.9982965 estimated iterations to convergence 192 setup time was (sec) 0.8500000 now iterating at: 11:49:16 rms-change max change #iterations 3.320445 148.8647 at 10iterations 1.409997 55.38133 at 20iterations 0.6049833 23.56890 at 30iterations 0.2583933 9.061394 at 40iterations 0.1107891 3.889080 at 50iterations 4.7508504E-02 1.825207 at 60iterations 2.0243671E-02 0.7414131 at 70iterations 8.6698551E-03 0.3519583 at 80iterations 3.7078124E-03 0.1399765 at 90iterations 1.5919744E-03 5.9959501E-02 at 100iterations 6.8303954E-04 2.4425030E-02 at 110iterations 2.9190545E-04 1.1950493E-02 at 120iterations finished qdiffx linear iterations at : 11:49:26 total time elapsed so far: 10.68000 # loops : 120 mean,max change (kT/e) : 2.9190545E-04 1.1950493E-02 energy calculations done at 10.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.85000 DelPhi exited at 11:49:26 10.853u 0.447s 0:11.62 97.1% 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 11:49:26 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 = 2587 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.557145 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): -14.41700 35.89400 ymin,ymax (A): 30.82600 74.91700 zmin,zma (A): -11.18100 51.46700 x,y,z range (A): 50.31100 44.09100 62.64800 scale (grids/A): 2.557145 object centre (A): 10.73850 52.87150 20.14300 number of atom coordinates read : 2587 total number of charged atoms : 2438 net assigned charge : -2.999990 assigned positive charge : 377.8216 centred at (gu) : 95.36133 93.54238 93.22351 assigned negative charge : -380.8224 centred at (gu) : 95.20946 93.55431 93.34290 start vw surface at 0.1100000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 139707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23571 grid for indexing accessible points = 1.400000 m= 63392 mr = 98516 m= 18590 mr = 49942 m= 2822 mr = 13894 m= 175 mr = 1808 m= 4 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.7099999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.200000 number of dielectric boundary points 60450 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 19496 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) : 1.704763 object centre at (A) : 10.73850 52.87150 20.14300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3381393E-02 -2.1051139E-02 midg,1,midg; midg,igrid,midg 3.3613931E-02 -9.3767628E-02 1,midg,midg; igrid,midg,midg -7.1566731E-02 9.2757447E-03 gauss-seidel spectral radius is 0.9991627 estimated iterations to convergence 273 setup time was (sec) 1.540000 now iterating at: 11:49:28 rms-change max change #iterations 8.313172 303.4895 at 10iterations 4.679354 125.5617 at 20iterations 2.618965 70.24049 at 30iterations 1.461291 37.04648 at 40iterations 0.8147366 22.30928 at 50iterations 0.4544200 10.06882 at 60iterations 0.2521772 5.927204 at 70iterations 0.1401141 3.027384 at 80iterations 7.7889264E-02 1.612666 at 90iterations 4.3259420E-02 0.9993954 at 100iterations 2.4013834E-02 0.5365810 at 110iterations 1.3303465E-02 0.2859812 at 120iterations 7.3736338E-03 0.1627221 at 130iterations 4.0862439E-03 0.1030197 at 140iterations 2.2620116E-03 4.8213959E-02 at 150iterations 1.2513419E-03 2.7986050E-02 at 160iterations 6.9332583E-04 1.5482903E-02 at 170iterations 3.8532628E-04 8.2135201E-03 at 180iterations finished qdiffx linear iterations at : 11:49:45 total time elapsed so far: 17.95000 # loops : 180 mean,max change (kT/e) : 3.8532628E-04 8.2135201E-03 energy calculations done at 17.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.11000 DelPhi exited at 11:49:45 18.119u 0.513s 0:18.96 98.2% 0+0k 0+0io 0pf+0w