Mon Oct 10 11:09:20 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 Mon Oct 10 2011 at 11:09:20 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 0.7468479 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): -21.38100 24.44500 ymin,ymax (A): -7.890000 38.45600 zmin,zma (A): -3.395000 44.27200 x,y,z range (A): 45.82600 46.34600 47.66700 scale (grids/A): 0.7468479 object centre (A): 1.532000 15.28300 20.43850 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 89.03117 89.69056 90.11938 assigned negative charge : -324.1440 centred at (gu) : 89.10654 89.72426 90.33669 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 8230 nv = 96 ne = 84 npr = 43922 no. pairs analyzed = 43922 no. exposed pairs = 2724 no. arc points = 19379 no. surface atoms = 919 nbur = 1209 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 565 mr = 4576 m= 5 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.1700000 number of dielectric boundary points 4109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1575 ## 125 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8638 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4549560E-07 -3.7270490E-07 midg,1,midg; midg,igrid,midg -6.6171815E-08 -1.3457584E-07 1,midg,midg; igrid,midg,midg -1.5493834E-08 -1.6086278E-07 gauss-seidel spectral radius is 0.9906600 estimated iterations to convergence 84 setup time was (sec) 0.3500000 now iterating at: 11:09:20 rms-change max change #iterations 0.2509283 34.41071 at 10iterations 3.4600962E-02 3.930773 at 20iterations 4.6591177E-03 0.5880470 at 30iterations 6.4786588E-04 7.9971313E-02 at 40iterations 8.9427602E-05 1.0913849E-02 at 50iterations finished qdiffx linear iterations at : 11:09:23 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 8.9427602E-05 1.0913849E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 11:09:24 3.407u 0.187s 0:03.87 92.5% 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 Mon Oct 10 2011 at 11:09:24 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 2.240544 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): -21.38100 24.44500 ymin,ymax (A): -7.890000 38.45600 zmin,zma (A): -3.395000 44.27200 x,y,z range (A): 45.82600 46.34600 47.66700 scale (grids/A): 2.240544 object centre (A): 1.532000 15.28300 20.43850 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 87.09327 89.07177 90.35821 assigned negative charge : -324.1440 centred at (gu) : 87.31943 89.17274 91.00985 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 86150 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19379 grid for indexing accessible points = 1.400000 m= 34448 mr = 59206 m= 7454 mr = 26206 m= 822 mr = 5267 m= 26 mr = 470 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 868 time to turn everything in is 0.4400000 number of dielectric boundary points 37750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 15853 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) : 0.7468479 object centre at (A) : 1.532000 15.28300 20.43850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8739164E-03 -0.1511628 midg,1,midg; midg,igrid,midg -3.0803502E-02 -1.9336443E-02 1,midg,midg; igrid,midg,midg 6.2859403E-03 -5.2238666E-03 gauss-seidel spectral radius is 0.9989452 estimated iterations to convergence 244 setup time was (sec) 0.6500000 now iterating at: 11:09:25 rms-change max change #iterations 5.185757 213.9603 at 10iterations 2.636005 90.21484 at 20iterations 1.351499 43.07711 at 30iterations 0.6942707 20.80983 at 40iterations 0.3558968 10.08720 at 50iterations 0.1827082 4.831572 at 60iterations 9.3716413E-02 2.879410 at 70iterations 4.7904901E-02 1.466974 at 80iterations 2.4597259E-02 0.7152925 at 90iterations 1.2615114E-02 0.3532429 at 100iterations 6.4510773E-03 0.1876020 at 110iterations 3.3181428E-03 8.8951111E-02 at 120iterations finished qdiffx linear iterations at : 11:09:32 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 3.3181428E-03 8.8951111E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 11:09:32 7.958u 0.199s 0:08.46 96.2% 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 Mon Oct 10 2011 at 11:09:32 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 3.360816 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): -21.38100 24.44500 ymin,ymax (A): -7.890000 38.45600 zmin,zma (A): -3.395000 44.27200 x,y,z range (A): 45.82600 46.34600 47.66700 scale (grids/A): 3.360816 object centre (A): 1.532000 15.28300 20.43850 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 85.63988 88.60747 90.53737 assigned negative charge : -324.1440 centred at (gu) : 85.97914 88.75907 91.51478 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 198190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19379 grid for indexing accessible points = 1.400000 m= 105371 mr = 142529 m= 45459 mr = 87203 m= 14267 mr = 37817 m= 3413 mr = 11544 m= 441 mr = 2623 m= 19 mr = 302 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 2741 time to turn everything in is 1.320000 number of dielectric boundary points 85142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 15912 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) : 2.240544 object centre at (A) : 1.532000 15.28300 20.43850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9531841E-02 -1.344617 midg,1,midg; midg,igrid,midg -0.2995928 -0.1145824 1,midg,midg; igrid,midg,midg 8.1256516E-02 -0.1495658 gauss-seidel spectral radius is 0.9993250 estimated iterations to convergence 304 setup time was (sec) 1.550000 now iterating at: 11:09:34 rms-change max change #iterations 11.15716 300.4803 at 10iterations 6.591931 136.6734 at 20iterations 3.908039 76.33926 at 30iterations 2.307025 43.43701 at 40iterations 1.361655 28.00238 at 50iterations 0.8029608 13.16365 at 60iterations 0.4737118 7.395611 at 70iterations 0.2794541 5.031300 at 80iterations 0.1645455 2.577597 at 90iterations 9.7005174E-02 1.531948 at 100iterations 5.6947544E-02 0.9260125 at 110iterations 3.3568699E-02 0.5371284 at 120iterations 1.9750157E-02 0.3125069 at 130iterations 1.1641656E-02 0.1800833 at 140iterations 6.8525048E-03 0.1143398 at 150iterations 4.0340857E-03 6.6055298E-02 at 160iterations 2.3789036E-03 3.4993887E-02 at 170iterations 1.4002082E-03 2.2049904E-02 at 180iterations finished qdiffx linear iterations at : 11:09:45 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 1.4002082E-03 2.2049904E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 11:09:46 13.115u 0.221s 0:13.60 98.0% 0+0k 0+0io 0pf+0w