Mon Oct 10 14:08:41 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+sph2.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 = amb2.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 14:08:41 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3367 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: 0.5425258 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): -11.37900 41.72800 ymin,ymax (A): -38.53200 27.08700 zmin,zma (A): -16.01400 34.93700 x,y,z range (A): 53.10700 65.61900 50.95100 scale (grids/A): 0.5425258 object centre (A): 15.17450 -5.722501 9.461500 number of atom coordinates read : 3367 total number of charged atoms : 3224 net assigned charge : 7.1823597E-06 assigned positive charge : 505.5415 centred at (gu) : 90.16575 91.62846 90.35847 assigned negative charge : -505.5429 centred at (gu) : 90.15343 91.58263 90.33298 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6498 nv = 96 ne = 84 npr = 67414 no. pairs analyzed = 67414 no. exposed pairs = 4177 no. arc points = 28598 no. surface atoms = 1416 nbur = 1951 mkacc time = 0.1800000 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 = 1.568000 m= 257 mr = 3525 m= 0 mr = 17 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2966 ## 429 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8507 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6041775E-10 1.7727474E-10 midg,1,midg; midg,igrid,midg -2.0696626E-10 4.4776388E-10 1,midg,midg; igrid,midg,midg -8.4352567E-11 7.8241094E-11 gauss-seidel spectral radius is 0.9825145 estimated iterations to convergence 62 setup time was (sec) 0.7200000 now iterating at: 14:08:42 rms-change max change #iterations 7.4411809E-02 15.97741 at 10iterations 4.9756067E-03 0.8142331 at 20iterations 3.9118144E-04 6.7860842E-02 at 30iterations 6.7469206E-05 1.1409760E-02 at 40iterations 1.8275063E-05 3.0860901E-03 at 50iterations finished qdiffx linear iterations at : 14:08:46 total time elapsed so far: 5.000000 # loops : 50 mean,max change (kT/e) : 1.8275063E-05 3.0860901E-03 energy calculations done at 5.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.180000 DelPhi exited at 14:08:47 5.185u 0.418s 0:06.20 90.1% 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 Mon Oct 10 2011 at 14:08:47 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3367 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: 1.627577 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): -11.37900 41.72800 ymin,ymax (A): -38.53200 27.08700 zmin,zma (A): -16.01400 34.93700 x,y,z range (A): 53.10700 65.61900 50.95100 scale (grids/A): 1.627577 object centre (A): 15.17450 -5.722501 9.461500 number of atom coordinates read : 3367 total number of charged atoms : 3224 net assigned charge : 7.1823597E-06 assigned positive charge : 505.5415 centred at (gu) : 90.49641 94.88445 91.07481 assigned negative charge : -505.5429 centred at (gu) : 90.45985 94.74755 90.99825 start vw surface at 0.1300000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72355 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28598 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23810 mr = 50565 m= 2551 mr = 16933 m= 63 mr = 1278 m= 0 mr = 10 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 29993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 359 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 24709 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) : 0.5425258 object centre at (A) : 15.17450 -5.722501 9.461500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3361976E-03 2.8907403E-03 midg,1,midg; midg,igrid,midg 8.8976854E-03 1.6186515E-02 1,midg,midg; igrid,midg,midg 1.4168074E-03 -1.0264604E-03 gauss-seidel spectral radius is 0.9982089 estimated iterations to convergence 188 setup time was (sec) 1.010000 now iterating at: 14:09:03 rms-change max change #iterations 3.528329 144.4158 at 10iterations 1.479457 55.44316 at 20iterations 0.6200624 24.03559 at 30iterations 0.2610494 8.588583 at 40iterations 0.1097698 3.815692 at 50iterations 4.6119682E-02 1.526135 at 60iterations 1.9348843E-02 0.6659393 at 70iterations 8.1440778E-03 0.2866898 at 80iterations 3.4506589E-03 0.1135864 at 90iterations 1.4533064E-03 5.1456451E-02 at 100iterations 6.2136014E-04 2.2740006E-02 at 110iterations 2.6993666E-04 9.1018677E-03 at 120iterations finished qdiffx linear iterations at : 14:09:14 total time elapsed so far: 11.83000 # loops : 120 mean,max change (kT/e) : 2.6993666E-04 9.1018677E-03 energy calculations done at 11.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.00000 DelPhi exited at 14:09:15 12.000u 0.584s 0:27.93 45.0% 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 14:09:15 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.441366 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): -11.37900 41.72800 ymin,ymax (A): -38.53200 27.08700 zmin,zma (A): -16.01400 34.93700 x,y,z range (A): 53.10700 65.61900 50.95100 scale (grids/A): 2.441366 object centre (A): 15.17450 -5.722501 9.461500 number of atom coordinates read : 3367 total number of charged atoms : 3224 net assigned charge : 7.1823597E-06 assigned positive charge : 505.5415 centred at (gu) : 90.74449 97.32632 91.61205 assigned negative charge : -505.5429 centred at (gu) : 90.68970 97.12103 91.49735 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 167853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28598 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 81677 mr = 123182 m= 24157 mr = 65662 m= 4096 mr = 18590 m= 335 mr = 2751 m= 3 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.540000 number of dielectric boundary points 67783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 25762 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) : 1.627577 object centre at (A) : 15.17450 -5.722501 9.461500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2181275E-02 6.3662700E-02 midg,1,midg; midg,igrid,midg 0.1415214 0.4488835 1,midg,midg; igrid,midg,midg 4.7620162E-02 -1.5564305E-03 gauss-seidel spectral radius is 0.9991524 estimated iterations to convergence 271 setup time was (sec) 1.960000 now iterating at: 14:09:18 rms-change max change #iterations 9.125884 356.4260 at 10iterations 5.146492 117.4290 at 20iterations 2.899241 63.12313 at 30iterations 1.619132 30.27963 at 40iterations 0.9030907 19.33493 at 50iterations 0.5024600 10.08125 at 60iterations 0.2796393 5.773613 at 70iterations 0.1549651 3.022194 at 80iterations 8.6017758E-02 1.610047 at 90iterations 4.7729373E-02 0.8842163 at 100iterations 2.6395597E-02 0.5382843 at 110iterations 1.4620634E-02 0.3069782 at 120iterations 8.0919508E-03 0.1559277 at 130iterations 4.4854353E-03 9.0622425E-02 at 140iterations 2.4865617E-03 4.7393799E-02 at 150iterations 1.3796040E-03 2.6214600E-02 at 160iterations 7.6946692E-04 1.6424179E-02 at 170iterations 4.3116041E-04 8.3951950E-03 at 180iterations finished qdiffx linear iterations at : 14:09:36 total time elapsed so far: 19.99000 # loops : 180 mean,max change (kT/e) : 4.3116041E-04 8.3951950E-03 energy calculations done at 19.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.16000 DelPhi exited at 14:09:36 20.164u 0.523s 0:21.55 95.9% 0+0k 0+0io 0pf+0w