Mon Oct 10 14:03:53 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 14:03:53 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 = 3278 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5579937 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): -9.788000 42.07400 ymin,ymax (A): -38.51900 25.28100 zmin,zma (A): -15.62100 34.01600 x,y,z range (A): 51.86200 63.80000 49.63700 scale (grids/A): 0.5579937 object centre (A): 16.14300 -6.619000 9.197500 number of atom coordinates read : 3278 total number of charged atoms : 3134 net assigned charge : 4.6938658E-06 assigned positive charge : 486.7547 centred at (gu) : 90.00218 91.80215 90.42503 assigned negative charge : -486.7560 centred at (gu) : 90.02395 91.74722 90.38348 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6608 nv = 96 ne = 84 npr = 67701 no. pairs analyzed = 67701 no. exposed pairs = 3894 no. arc points = 27440 no. surface atoms = 1326 nbur = 1952 mkacc time = 0.1200000 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 = 1.540000 m= 266 mr = 3645 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3217 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2766 ## 346 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8572 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3646192E-10 5.0074245E-10 midg,1,midg; midg,igrid,midg -4.1011664E-10 9.4002839E-10 1,midg,midg; igrid,midg,midg 2.2970466E-10 -2.6034136E-10 gauss-seidel spectral radius is 0.9834513 estimated iterations to convergence 64 setup time was (sec) 0.4200000 now iterating at: 14:03:53 rms-change max change #iterations 8.4693603E-02 13.79868 at 10iterations 6.0922997E-03 0.9538889 at 20iterations 4.9647159E-04 8.0825806E-02 at 30iterations 6.3509091E-05 1.0667801E-02 at 40iterations 1.3796794E-05 2.4099350E-03 at 50iterations finished qdiffx linear iterations at : 14:03:56 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.3796794E-05 2.4099350E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:03:57 3.392u 0.199s 0:04.13 86.6% 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 14:03:57 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 = 3278 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.673981 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): -9.788000 42.07400 ymin,ymax (A): -38.51900 25.28100 zmin,zma (A): -15.62100 34.01600 x,y,z range (A): 51.86200 63.80000 49.63700 scale (grids/A): 1.673981 object centre (A): 16.14300 -6.619000 9.197500 number of atom coordinates read : 3278 total number of charged atoms : 3134 net assigned charge : 4.6938658E-06 assigned positive charge : 486.7547 centred at (gu) : 90.00591 95.40560 91.27417 assigned negative charge : -486.7560 centred at (gu) : 90.07156 95.24134 91.15003 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27440 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23566 mr = 51451 m= 2426 mr = 16739 m= 72 mr = 1237 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 440 time to turn everything in is 0.3500000 number of dielectric boundary points 29929 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 297 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 24155 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) : 0.5579937 object centre at (A) : 16.14300 -6.619000 9.197500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0414602E-03 4.2984779E-03 midg,1,midg; midg,igrid,midg 8.9294612E-03 5.6622326E-03 1,midg,midg; igrid,midg,midg 5.1598698E-03 9.3737216E-04 gauss-seidel spectral radius is 0.9982963 estimated iterations to convergence 192 setup time was (sec) 0.5600000 now iterating at: 14:03:58 rms-change max change #iterations 3.654323 162.3365 at 10iterations 1.559980 56.92872 at 20iterations 0.6718242 24.67381 at 30iterations 0.2876709 9.729421 at 40iterations 0.1237340 4.354042 at 50iterations 5.3114802E-02 1.831589 at 60iterations 2.2800427E-02 0.7549372 at 70iterations 9.7842505E-03 0.3429623 at 80iterations 4.2089215E-03 0.1541681 at 90iterations 1.8124605E-03 5.9036255E-02 at 100iterations 7.8299013E-04 2.7273178E-02 at 110iterations 3.4003978E-04 1.0587692E-02 at 120iterations finished qdiffx linear iterations at : 14:04:05 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 3.4003978E-04 1.0587692E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 14:04:05 7.694u 0.188s 0:08.28 95.0% 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 14:04:05 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 = 3278 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.510972 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): -9.788000 42.07400 ymin,ymax (A): -38.51900 25.28100 zmin,zma (A): -15.62100 34.01600 x,y,z range (A): 51.86200 63.80000 49.63700 scale (grids/A): 2.510972 object centre (A): 16.14300 -6.619000 9.197500 number of atom coordinates read : 3278 total number of charged atoms : 3134 net assigned charge : 4.6938658E-06 assigned positive charge : 486.7547 centred at (gu) : 90.00866 98.10808 91.91095 assigned negative charge : -486.7560 centred at (gu) : 90.10730 97.86192 91.72496 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 170360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27440 grid for indexing accessible points = 1.400000 m= 81240 mr = 125358 m= 23498 mr = 65663 m= 3894 mr = 18128 m= 305 mr = 2548 m= 10 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 1455 time to turn everything in is 0.8500000 number of dielectric boundary points 67504 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 25051 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) : 1.673981 object centre at (A) : 16.14300 -6.619000 9.197500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1319457 7.4121207E-02 midg,1,midg; midg,igrid,midg 0.2075220 1.8698957E-02 1,midg,midg; igrid,midg,midg 9.5574573E-02 2.7699782E-02 gauss-seidel spectral radius is 0.9991723 estimated iterations to convergence 275 setup time was (sec) 1.090000 now iterating at: 14:04:06 rms-change max change #iterations 9.226707 284.4378 at 10iterations 5.212937 114.7381 at 20iterations 2.937479 73.27595 at 30iterations 1.649682 32.28631 at 40iterations 0.9226328 17.55466 at 50iterations 0.5150568 11.86753 at 60iterations 0.2883514 5.630048 at 70iterations 0.1609213 3.147642 at 80iterations 8.9695565E-02 2.025295 at 90iterations 5.0051920E-02 0.9447861 at 100iterations 2.7871234E-02 0.5340791 at 110iterations 1.5507727E-02 0.2922268 at 120iterations 8.6604673E-03 0.1705580 at 130iterations 4.8212195E-03 9.3484402E-02 at 140iterations 2.6919961E-03 5.5327415E-02 at 150iterations 1.5040687E-03 2.7169943E-02 at 160iterations 8.4281689E-04 1.8218994E-02 at 170iterations 4.7504256E-04 1.0417819E-02 at 180iterations finished qdiffx linear iterations at : 14:04:17 total time elapsed so far: 12.14000 # loops : 180 mean,max change (kT/e) : 4.7504256E-04 1.0417819E-02 energy calculations done at 12.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 14:04:18 12.276u 0.215s 0:13.13 95.0% 0+0k 0+0io 0pf+0w