Mon Oct 10 09:50:35 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 09:50:36 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 = 2833 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5812909 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): -17.41200 36.19800 ymin,ymax (A): -63.20800 -4.714000 zmin,zma (A): -4.153000 57.09000 x,y,z range (A): 53.61000 58.49400 61.24300 scale (grids/A): 0.5812909 object centre (A): 9.392999 -33.96100 26.46850 number of atom coordinates read : 2833 total number of charged atoms : 2681 net assigned charge : 4.000010 assigned positive charge : 415.8819 centred at (gu) : 89.13133 89.43935 87.68629 assigned negative charge : -411.8823 centred at (gu) : 89.26743 89.33752 87.48483 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6458 nv = 96 ne = 84 npr = 54831 no. pairs analyzed = 54831 no. exposed pairs = 4295 no. arc points = 31680 no. surface atoms = 1404 nbur = 1429 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= 328 mr = 2811 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3087 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8127 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8937344E-09 3.0159877E-09 midg,1,midg; midg,igrid,midg -1.3370968E-09 2.7497176E-09 1,midg,midg; igrid,midg,midg 4.7116657E-09 -1.5450394E-09 gauss-seidel spectral radius is 0.9847301 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 09:50:36 rms-change max change #iterations 9.2923716E-02 15.35728 at 10iterations 7.0044473E-03 1.448349 at 20iterations 5.6548370E-04 9.9472046E-02 at 30iterations 4.7163881E-05 6.9904327E-03 at 40iterations 5.0192489E-06 6.4849854E-04 at 50iterations finished qdiffx linear iterations at : 09:50:39 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 5.0192489E-06 6.4849854E-04 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 09:50:40 3.599u 0.212s 0:04.21 90.2% 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 09:50:40 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 = 2833 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.743873 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): -17.41200 36.19800 ymin,ymax (A): -63.20800 -4.714000 zmin,zma (A): -4.153000 57.09000 x,y,z range (A): 53.61000 58.49400 61.24300 scale (grids/A): 1.743873 object centre (A): 9.392999 -33.96100 26.46850 number of atom coordinates read : 2833 total number of charged atoms : 2681 net assigned charge : 4.000010 assigned positive charge : 415.8819 centred at (gu) : 87.39359 88.31744 83.05834 assigned negative charge : -411.8823 centred at (gu) : 87.80203 88.01220 82.45406 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31680 grid for indexing accessible points = 1.400000 m= 21309 mr = 42374 m= 2771 mr = 13287 m= 120 mr = 1221 m= 0 mr = 23 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.5500000 number of dielectric boundary points 36781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 268 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 20823 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) : 0.5812909 object centre at (A) : 9.392999 -33.96100 26.46850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1537760E-02 1.8930357E-02 midg,1,midg; midg,igrid,midg 1.9511351E-02 3.8306478E-02 1,midg,midg; igrid,midg,midg 1.6168244E-02 -3.0996723E-03 gauss-seidel spectral radius is 0.9984211 estimated iterations to convergence 200 setup time was (sec) 0.8800000 now iterating at: 09:50:41 rms-change max change #iterations 3.691692 158.2683 at 10iterations 1.624641 78.96529 at 20iterations 0.7129802 25.93773 at 30iterations 0.3153608 10.54628 at 40iterations 0.1383828 4.830774 at 50iterations 6.1272547E-02 2.025419 at 60iterations 2.6917851E-02 0.9004307 at 70iterations 1.1897014E-02 0.4126987 at 80iterations 5.2473275E-03 0.1857271 at 90iterations 2.3156439E-03 8.1848145E-02 at 100iterations 1.0235553E-03 3.3161163E-02 at 110iterations 4.5033390E-04 1.5974998E-02 at 120iterations finished qdiffx linear iterations at : 09:50:48 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 4.5033390E-04 1.5974998E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 09:50:48 8.037u 0.243s 0:08.59 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 09:50:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2833 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.615809 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): -17.41200 36.19800 ymin,ymax (A): -63.20800 -4.714000 zmin,zma (A): -4.153000 57.09000 x,y,z range (A): 53.61000 58.49400 61.24300 scale (grids/A): 2.615809 object centre (A): 9.392999 -33.96100 26.46850 number of atom coordinates read : 2833 total number of charged atoms : 2681 net assigned charge : 4.000010 assigned positive charge : 415.8819 centred at (gu) : 86.09025 87.47602 79.58746 assigned negative charge : -411.8823 centred at (gu) : 86.70293 87.01826 78.68102 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 160280 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31680 grid for indexing accessible points = 1.400000 m= 70951 mr = 104605 m= 22282 mr = 52434 m= 4371 mr = 15583 m= 472 mr = 2612 m= 17 mr = 233 m= 0 mr = 4 time to grow re-entrant surface = 0.7599999 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 1.330000 number of dielectric boundary points 82902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 21438 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) : 1.743873 object centre at (A) : 9.392999 -33.96100 26.46850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2329639 0.2816442 midg,1,midg; midg,igrid,midg 0.5684205 0.5092857 1,midg,midg; igrid,midg,midg 0.1580501 -9.8802941E-03 gauss-seidel spectral radius is 0.9992261 estimated iterations to convergence 284 setup time was (sec) 1.670000 now iterating at: 09:50:50 rms-change max change #iterations 9.363257 272.0453 at 10iterations 5.532704 153.3154 at 20iterations 3.237026 94.13818 at 30iterations 1.875232 53.60752 at 40iterations 1.077237 30.31324 at 50iterations 0.6185982 14.13577 at 60iterations 0.3543291 9.421730 at 70iterations 0.2030596 5.234293 at 80iterations 0.1156928 2.771683 at 90iterations 6.5987490E-02 1.560276 at 100iterations 3.7633795E-02 0.8564451 at 110iterations 2.1387490E-02 0.5087450 at 120iterations 1.2152955E-02 0.2809677 at 130iterations 6.8998975E-03 0.1596985 at 140iterations 3.9185993E-03 7.7515364E-02 at 150iterations 2.2311620E-03 4.4247150E-02 at 160iterations 1.2622051E-03 2.6674271E-02 at 170iterations 7.1707281E-04 1.5242577E-02 at 180iterations finished qdiffx linear iterations at : 09:51:04 total time elapsed so far: 14.88000 # loops : 180 mean,max change (kT/e) : 7.1707281E-04 1.5242577E-02 energy calculations done at 14.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.08000 DelPhi exited at 09:51:04 15.080u 0.258s 0:15.75 97.3% 0+0k 0+0io 0pf+0w