Sun Oct 9 14:16:36 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 Sun Oct 9 2011 at 14:16:36 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 = 2816 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: 0.5566501 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): -1.540000 54.90600 ymin,ymax (A): -7.645000 40.65100 zmin,zma (A): -16.42500 47.52900 x,y,z range (A): 56.44600 48.29600 63.95400 scale (grids/A): 0.5566501 object centre (A): 26.68300 16.50300 15.55200 number of atom coordinates read : 2816 total number of charged atoms : 2675 net assigned charge : 6.000013 assigned positive charge : 427.5853 centred at (gu) : 88.49786 90.23804 89.27553 assigned negative charge : -421.5864 centred at (gu) : 88.45712 90.10562 89.32336 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5702 nv = 96 ne = 84 npr = 55619 no. pairs analyzed = 55619 no. exposed pairs = 3656 no. arc points = 25513 no. surface atoms = 1221 nbur = 1595 mkacc time = 9.9999994E-02 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= 242 mr = 2890 m= 0 mr = 9 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3045 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2664 ## 346 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7370 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1958660E-09 9.9822005E-11 midg,1,midg; midg,igrid,midg -6.4847328E-10 1.8784454E-09 1,midg,midg; igrid,midg,midg 2.4900440E-10 6.5612565E-10 gauss-seidel spectral radius is 0.9833436 estimated iterations to convergence 64 setup time was (sec) 0.3900000 now iterating at: 14:16:37 rms-change max change #iterations 7.8207687E-02 18.04634 at 10iterations 5.3451457E-03 0.8914051 at 20iterations 3.8147287E-04 7.0474625E-02 at 30iterations 2.8317372E-05 4.7225952E-03 at 40iterations 2.3391667E-06 3.7002563E-04 at 50iterations finished qdiffx linear iterations at : 14:16:39 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.3391667E-06 3.7002563E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:16:40 3.383u 0.170s 0:03.82 92.9% 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 Sun Oct 9 2011 at 14:16:40 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 = 2816 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: 1.669950 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): -1.540000 54.90600 ymin,ymax (A): -7.645000 40.65100 zmin,zma (A): -16.42500 47.52900 x,y,z range (A): 56.44600 48.29600 63.95400 scale (grids/A): 1.669950 object centre (A): 26.68300 16.50300 15.55200 number of atom coordinates read : 2816 total number of charged atoms : 2675 net assigned charge : 6.000013 assigned positive charge : 427.5853 centred at (gu) : 85.49277 90.71297 87.82565 assigned negative charge : -421.5864 centred at (gu) : 85.37092 90.31665 87.96987 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 62880 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25513 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19119 mr = 41949 m= 1966 mr = 12886 m= 56 mr = 873 m= 3 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 204 time to turn everything in is 0.3200000 number of dielectric boundary points 28314 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 311 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20573 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) : 0.5566501 object centre at (A) : 26.68300 16.50300 15.55200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3991540E-02 1.4084669E-02 midg,1,midg; midg,igrid,midg -4.4412844E-04 9.6988454E-03 1,midg,midg; igrid,midg,midg -1.6955256E-02 -9.2847052E-04 gauss-seidel spectral radius is 0.9982566 estimated iterations to convergence 190 setup time was (sec) 0.5200000 now iterating at: 14:16:41 rms-change max change #iterations 3.376947 154.0346 at 10iterations 1.425791 53.16229 at 20iterations 0.6029469 24.96171 at 30iterations 0.2558224 9.161617 at 40iterations 0.1077828 3.696579 at 50iterations 4.5785759E-02 1.569412 at 60iterations 1.9468844E-02 0.7848947 at 70iterations 8.2762642E-03 0.3374672 at 80iterations 3.5164058E-03 0.1322708 at 90iterations 1.4921741E-03 5.0956726E-02 at 100iterations 6.3605531E-04 2.4658203E-02 at 110iterations 2.7038067E-04 9.8419189E-03 at 120iterations finished qdiffx linear iterations at : 14:16:48 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 2.7038067E-04 9.8419189E-03 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 14:16:48 7.643u 0.199s 0:08.11 96.5% 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 Sun Oct 9 2011 at 14:16:48 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 = 2816 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: 2.504925 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): -1.540000 54.90600 ymin,ymax (A): -7.645000 40.65100 zmin,zma (A): -16.42500 47.52900 x,y,z range (A): 56.44600 48.29600 63.95400 scale (grids/A): 2.504925 object centre (A): 26.68300 16.50300 15.55200 number of atom coordinates read : 2816 total number of charged atoms : 2675 net assigned charge : 6.000013 assigned positive charge : 427.5853 centred at (gu) : 83.23896 91.06934 86.73822 assigned negative charge : -421.5864 centred at (gu) : 83.05637 90.47492 86.95478 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 145811 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25513 grid for indexing accessible points = 1.400000 m= 66736 mr = 102825 m= 18568 mr = 52185 m= 2904 mr = 13433 m= 262 mr = 1800 m= 6 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 643 time to turn everything in is 0.7500000 number of dielectric boundary points 63950 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 21375 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) : 1.669950 object centre at (A) : 26.68300 16.50300 15.55200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6734051 0.2965794 midg,1,midg; midg,igrid,midg 2.2132960E-03 0.1133694 1,midg,midg; igrid,midg,midg -0.2223419 -3.2504957E-02 gauss-seidel spectral radius is 0.9991573 estimated iterations to convergence 272 setup time was (sec) 0.9900000 now iterating at: 14:16:49 rms-change max change #iterations 8.718615 292.7533 at 10iterations 5.015619 141.5825 at 20iterations 2.858268 92.15879 at 30iterations 1.610985 40.65453 at 40iterations 0.9054335 23.67521 at 50iterations 0.5067897 12.92370 at 60iterations 0.2834547 7.161112 at 70iterations 0.1579157 3.360373 at 80iterations 8.7800898E-02 2.028227 at 90iterations 4.8930179E-02 1.053665 at 100iterations 2.7158925E-02 0.5616137 at 110iterations 1.5033123E-02 0.3169203 at 120iterations 8.3673792E-03 0.1789722 at 130iterations 4.6342481E-03 0.1002364 at 140iterations 2.5670971E-03 6.2599897E-02 at 150iterations 1.4247862E-03 3.1517982E-02 at 160iterations 7.9346675E-04 1.5681267E-02 at 170iterations 4.4102641E-04 1.0669708E-02 at 180iterations finished qdiffx linear iterations at : 14:17:00 total time elapsed so far: 12.09000 # loops : 180 mean,max change (kT/e) : 4.4102641E-04 1.0669708E-02 energy calculations done at 12.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 14:17:01 12.228u 0.198s 0:12.69 97.7% 0+0k 0+0io 0pf+0w