Tue Oct 11 06:49:55 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 Tue Oct 11 2011 at 06:49:55 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 = 2985 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5442510 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): -20.11900 45.29200 ymin,ymax (A): 19.50100 76.76500 zmin,zma (A): -70.33700 -20.48100 x,y,z range (A): 65.41100 57.26400 49.85600 scale (grids/A): 0.5442510 object centre (A): 12.58650 48.13300 -45.40900 number of atom coordinates read : 2985 total number of charged atoms : 2844 net assigned charge : -3.499989 assigned positive charge : 434.8865 centred at (gu) : 89.56766 89.47218 89.81264 assigned negative charge : -438.3871 centred at (gu) : 89.55861 89.63695 89.83164 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5718 nv = 96 ne = 84 npr = 61981 no. pairs analyzed = 61981 no. exposed pairs = 3744 no. arc points = 26437 no. surface atoms = 1269 nbur = 1716 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 = 1.596000 m= 245 mr = 2955 m= 0 mr = 11 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2997 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2647 ## 326 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7460 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.6225992E-11 -3.1117539E-10 midg,1,midg; midg,igrid,midg 8.9641894E-10 -1.0889735E-09 1,midg,midg; igrid,midg,midg -2.9382294E-10 -1.3830095E-10 gauss-seidel spectral radius is 0.9825989 estimated iterations to convergence 62 setup time was (sec) 0.5800000 now iterating at: 06:49:56 rms-change max change #iterations 7.2187148E-02 13.19059 at 10iterations 4.9209264E-03 0.7728653 at 20iterations 3.1611527E-04 5.3998947E-02 at 30iterations 2.2061118E-05 4.4784546E-03 at 40iterations 1.6087409E-06 2.6464462E-04 at 50iterations finished qdiffx linear iterations at : 06:49:59 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.6087409E-06 2.6464462E-04 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 06:49:59 3.360u 0.180s 0:04.23 83.6% 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 Tue Oct 11 2011 at 06:50:00 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 = 2985 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.632753 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): -20.11900 45.29200 ymin,ymax (A): 19.50100 76.76500 zmin,zma (A): -70.33700 -20.48100 x,y,z range (A): 65.41100 57.26400 49.85600 scale (grids/A): 1.632753 object centre (A): 12.58650 48.13300 -45.40900 number of atom coordinates read : 2985 total number of charged atoms : 2844 net assigned charge : -3.499989 assigned positive charge : 434.8865 centred at (gu) : 88.70210 88.41627 89.43739 assigned negative charge : -438.3871 centred at (gu) : 88.67552 88.91045 89.49447 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 63175 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26437 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19782 mr = 42373 m= 2173 mr = 13799 m= 51 mr = 1053 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 27954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 284 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 21822 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) : 0.5442510 object centre at (A) : 12.58650 48.13300 -45.40900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0339404E-03 7.7730939E-03 midg,1,midg; midg,igrid,midg -4.8783809E-04 -3.0928658E-04 1,midg,midg; igrid,midg,midg 2.6690273E-03 -3.1841099E-02 gauss-seidel spectral radius is 0.9981918 estimated iterations to convergence 187 setup time was (sec) 0.7600000 now iterating at: 06:50:01 rms-change max change #iterations 3.275440 152.1232 at 10iterations 1.366477 53.28942 at 20iterations 0.5704437 21.92281 at 30iterations 0.2373936 9.373123 at 40iterations 9.9589221E-02 3.759251 at 50iterations 4.1484036E-02 1.467048 at 60iterations 1.7351126E-02 0.6209164 at 70iterations 7.2483141E-03 0.2684848 at 80iterations 3.0341670E-03 0.1148510 at 90iterations 1.2678435E-03 4.4326782E-02 at 100iterations 5.3176749E-04 1.9054413E-02 at 110iterations 2.2159393E-04 8.1755519E-03 at 120iterations finished qdiffx linear iterations at : 06:50:07 total time elapsed so far: 7.130000 # loops : 120 mean,max change (kT/e) : 2.2159393E-04 8.1755519E-03 energy calculations done at 7.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 06:50:08 7.288u 0.251s 0:08.49 88.6% 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 Tue Oct 11 2011 at 06:50:08 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 = 2985 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.449130 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): -20.11900 45.29200 ymin,ymax (A): 19.50100 76.76500 zmin,zma (A): -70.33700 -20.48100 x,y,z range (A): 65.41100 57.26400 49.85600 scale (grids/A): 2.449130 object centre (A): 12.58650 48.13300 -45.40900 number of atom coordinates read : 2985 total number of charged atoms : 2844 net assigned charge : -3.499989 assigned positive charge : 434.8865 centred at (gu) : 88.05296 87.62428 89.15581 assigned negative charge : -438.3871 centred at (gu) : 88.01310 88.36547 89.24164 start vw surface at 0.1900000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 146491 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26437 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67755 mr = 103549 m= 20035 mr = 53857 m= 3347 mr = 15180 m= 205 mr = 2157 m= 2 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.120000 number of dielectric boundary points 63009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 22723 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) : 1.632753 object centre at (A) : 12.58650 48.13300 -45.40900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3670439E-02 0.1865583 midg,1,midg; midg,igrid,midg -3.4774728E-03 3.6795374E-02 1,midg,midg; igrid,midg,midg 1.1365066E-02 -0.6407970 gauss-seidel spectral radius is 0.9991430 estimated iterations to convergence 270 setup time was (sec) 1.420000 now iterating at: 06:50:10 rms-change max change #iterations 8.451565 299.1968 at 10iterations 4.731025 134.5094 at 20iterations 2.636556 60.59024 at 30iterations 1.462175 31.51589 at 40iterations 0.8108675 18.72614 at 50iterations 0.4469297 8.807224 at 60iterations 0.2474659 5.511578 at 70iterations 0.1361181 2.970545 at 80iterations 7.5011857E-02 1.654911 at 90iterations 4.1368883E-02 0.8510551 at 100iterations 2.2689987E-02 0.4480515 at 110iterations 1.2501474E-02 0.2682619 at 120iterations 6.8786219E-03 0.1402912 at 130iterations 3.7877890E-03 8.1493378E-02 at 140iterations 2.0826450E-03 4.3690681E-02 at 150iterations 1.1447623E-03 2.5112152E-02 at 160iterations 6.2875112E-04 1.3540745E-02 at 170iterations 3.4546616E-04 7.4863434E-03 at 180iterations finished qdiffx linear iterations at : 06:50:20 total time elapsed so far: 11.55000 # loops : 180 mean,max change (kT/e) : 3.4546616E-04 7.4863434E-03 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.73000 DelPhi exited at 06:50:20 11.737u 0.231s 0:12.38 96.6% 0+0k 0+0io 0pf+0w