Mon Oct 10 17:05:48 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 17:05:48 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 = 2682 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5542840 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): -40.49500 6.727000 ymin,ymax (A): -9.829000 41.69500 zmin,zma (A): -61.76200 2.465000 x,y,z range (A): 47.22200 51.52400 64.22701 scale (grids/A): 0.5542840 object centre (A): -16.88400 15.93300 -29.64850 number of atom coordinates read : 2682 total number of charged atoms : 2543 net assigned charge : 6.000025 assigned positive charge : 399.6636 centred at (gu) : 89.70772 89.73275 90.59783 assigned negative charge : -393.6646 centred at (gu) : 89.68578 89.63824 90.53686 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5356 nv = 96 ne = 84 npr = 53569 no. pairs analyzed = 53569 no. exposed pairs = 3650 no. arc points = 25892 no. surface atoms = 1229 nbur = 1453 mkacc time = 0.1400000 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= 234 mr = 2601 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2656 ## 375 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7036 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3559245E-11 1.1547856E-09 midg,1,midg; midg,igrid,midg -2.6849856E-10 1.1820290E-09 1,midg,midg; igrid,midg,midg 3.6265022E-10 6.4306327E-10 gauss-seidel spectral radius is 0.9831951 estimated iterations to convergence 63 setup time was (sec) 0.6100000 now iterating at: 17:05:49 rms-change max change #iterations 7.2657630E-02 13.28535 at 10iterations 5.0983839E-03 0.9354973 at 20iterations 3.5438870E-04 5.8540344E-02 at 30iterations 2.6640027E-05 4.5168400E-03 at 40iterations 2.3540670E-06 4.5919418E-04 at 50iterations finished qdiffx linear iterations at : 17:05:54 total time elapsed so far: 5.200000 # loops : 50 mean,max change (kT/e) : 2.3540670E-06 4.5919418E-04 energy calculations done at 5.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.380000 DelPhi exited at 17:05:54 5.385u 0.512s 0:06.37 92.4% 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 17:05:54 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 = 2682 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.662852 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): -40.49500 6.727000 ymin,ymax (A): -9.829000 41.69500 zmin,zma (A): -61.76200 2.465000 x,y,z range (A): 47.22200 51.52400 64.22701 scale (grids/A): 1.662852 object centre (A): -16.88400 15.93300 -29.64850 number of atom coordinates read : 2682 total number of charged atoms : 2543 net assigned charge : 6.000025 assigned positive charge : 399.6636 centred at (gu) : 89.12241 89.19762 91.79276 assigned negative charge : -393.6646 centred at (gu) : 89.05733 88.91442 91.61061 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25892 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17481 mr = 38781 m= 1727 mr = 11352 m= 52 mr = 765 m= 0 mr = 2 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 27913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 268 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19580 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) : 0.5542840 object centre at (A) : -16.88400 15.93300 -29.64850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3219062E-02 1.7956629E-02 midg,1,midg; midg,igrid,midg -9.8317079E-03 2.7599924E-03 1,midg,midg; igrid,midg,midg 1.0067793E-03 6.5579717E-03 gauss-seidel spectral radius is 0.9982259 estimated iterations to convergence 189 setup time was (sec) 0.8400000 now iterating at: 17:05:56 rms-change max change #iterations 3.229652 165.8301 at 10iterations 1.347396 56.91227 at 20iterations 0.5657747 21.76928 at 30iterations 0.2380066 9.758157 at 40iterations 0.1001343 4.240559 at 50iterations 4.2143989E-02 1.563550 at 60iterations 1.7741647E-02 0.6806865 at 70iterations 7.4597360E-03 0.2769814 at 80iterations 3.1505080E-03 0.1489663 at 90iterations 1.3261440E-03 5.3431511E-02 at 100iterations 5.5799610E-04 2.1409035E-02 at 110iterations 2.3541703E-04 8.5506439E-03 at 120iterations finished qdiffx linear iterations at : 17:06:06 total time elapsed so far: 10.97000 # loops : 120 mean,max change (kT/e) : 2.3541703E-04 8.5506439E-03 energy calculations done at 10.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.16000 DelPhi exited at 17:06:07 11.162u 0.550s 0:12.14 96.4% 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 17:06:07 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 = 2682 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.494278 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): -40.49500 6.727000 ymin,ymax (A): -9.829000 41.69500 zmin,zma (A): -61.76200 2.465000 x,y,z range (A): 47.22200 51.52400 64.22701 scale (grids/A): 2.494278 object centre (A): -16.88400 15.93300 -29.64850 number of atom coordinates read : 2682 total number of charged atoms : 2543 net assigned charge : 6.000025 assigned positive charge : 399.6636 centred at (gu) : 88.68330 88.79626 92.68886 assigned negative charge : -393.6646 centred at (gu) : 88.58605 88.37159 92.41573 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 138140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25892 grid for indexing accessible points = 1.400000 m= 60837 mr = 95153 m= 16411 mr = 46652 m= 2546 mr = 11710 m= 166 mr = 1569 m= 4 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 62988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 20327 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) : 1.662852 object centre at (A) : -16.88400 15.93300 -29.64850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5907493 0.2214669 midg,1,midg; midg,igrid,midg -0.1139057 6.0243714E-03 1,midg,midg; igrid,midg,midg 5.2748760E-03 8.8281713E-02 gauss-seidel spectral radius is 0.9991494 estimated iterations to convergence 271 setup time was (sec) 1.540000 now iterating at: 17:06:09 rms-change max change #iterations 8.458339 343.4576 at 10iterations 4.816313 120.8927 at 20iterations 2.709479 69.60272 at 30iterations 1.515837 37.01119 at 40iterations 0.8433363 19.35663 at 50iterations 0.4684841 10.40122 at 60iterations 0.2587610 5.959308 at 70iterations 0.1430591 3.510592 at 80iterations 7.9123572E-02 1.899077 at 90iterations 4.3740310E-02 0.9495935 at 100iterations 2.4137586E-02 0.5365257 at 110iterations 1.3314745E-02 0.2841911 at 120iterations 7.3307026E-03 0.1763496 at 130iterations 4.0326323E-03 9.4413757E-02 at 140iterations 2.2267227E-03 4.6889782E-02 at 150iterations 1.2255186E-03 2.6849717E-02 at 160iterations 6.7525246E-04 1.6311646E-02 at 170iterations 3.7277158E-04 8.5363388E-03 at 180iterations finished qdiffx linear iterations at : 17:06:22 total time elapsed so far: 14.75000 # loops : 180 mean,max change (kT/e) : 3.7277158E-04 8.5363388E-03 energy calculations done at 14.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.93000 DelPhi exited at 17:06:23 14.937u 0.445s 0:15.95 96.3% 0+0k 0+0io 0pf+0w