Tue Oct 11 06:28:21 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 Tue Oct 11 2011 at 06:28:21 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2025 !!! WARNING: SEP 194 has a net charge of -0.4750 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: 0.7317274 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): -19.68700 23.83300 ymin,ymax (A): -40.36000 -0.6320001 zmin,zma (A): -36.93000 11.72200 x,y,z range (A): 43.52000 39.72800 48.65200 scale (grids/A): 0.7317274 object centre (A): 2.073000 -20.49600 -12.60400 number of atom coordinates read : 2025 total number of charged atoms : 1897 net assigned charge : 6.025006 assigned positive charge : 307.6071 centred at (gu) : 89.93620 89.40580 91.09801 assigned negative charge : -301.5822 centred at (gu) : 89.76102 89.44324 91.19016 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7574 nv = 96 ne = 84 npr = 40342 no. pairs analyzed = 40342 no. exposed pairs = 2481 no. arc points = 17003 no. surface atoms = 843 nbur = 1182 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 589 mr = 4454 m= 12 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3594 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1488 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7992 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3295346E-07 1.6576033E-08 midg,1,midg; midg,igrid,midg 1.3351723E-07 5.3338955E-08 1,midg,midg; igrid,midg,midg -5.4869528E-08 2.2557303E-07 gauss-seidel spectral radius is 0.9902551 estimated iterations to convergence 82 setup time was (sec) 0.5100000 now iterating at: 06:28:22 rms-change max change #iterations 0.2308856 36.49680 at 10iterations 3.0458266E-02 3.753012 at 20iterations 4.3262714E-03 0.5182924 at 30iterations 7.1110221E-04 9.2295647E-02 at 40iterations 1.7615331E-04 2.5053024E-02 at 50iterations finished qdiffx linear iterations at : 06:28:24 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.7615331E-04 2.5053024E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 06:28:25 3.463u 0.174s 0:03.98 91.2% 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 06:28:25 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2025 !!! WARNING: SEP 194 has a net charge of -0.4750 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: 2.195182 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): -19.68700 23.83300 ymin,ymax (A): -40.36000 -0.6320001 zmin,zma (A): -36.93000 11.72200 x,y,z range (A): 43.52000 39.72800 48.65200 scale (grids/A): 2.195182 object centre (A): 2.073000 -20.49600 -12.60400 number of atom coordinates read : 2025 total number of charged atoms : 1897 net assigned charge : 6.025006 assigned positive charge : 307.6071 centred at (gu) : 89.80854 88.21756 93.29396 assigned negative charge : -301.5822 centred at (gu) : 89.28321 88.32981 93.57062 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79354 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17003 grid for indexing accessible points = 1.400000 m= 33862 mr = 56851 m= 7293 mr = 26138 m= 791 mr = 4935 m= 29 mr = 442 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 32961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15087 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) : 0.7317274 object centre at (A) : 2.073000 -20.49600 -12.60400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7907580E-02 1.4669969E-02 midg,1,midg; midg,igrid,midg 3.7143067E-02 7.4438225E-03 1,midg,midg; igrid,midg,midg 1.7604131E-02 5.4303277E-02 gauss-seidel spectral radius is 0.9988927 estimated iterations to convergence 238 setup time was (sec) 0.9400000 now iterating at: 06:28:26 rms-change max change #iterations 4.794561 188.9730 at 10iterations 2.418927 84.43024 at 20iterations 1.229026 45.56673 at 30iterations 0.6231482 18.48458 at 40iterations 0.3142195 9.944340 at 50iterations 0.1593340 4.448469 at 60iterations 8.0497518E-02 2.431030 at 70iterations 4.1035857E-02 1.226461 at 80iterations 2.0862233E-02 0.6426773 at 90iterations 1.0616332E-02 0.3207140 at 100iterations 5.4613715E-03 0.1556683 at 110iterations 2.8361040E-03 8.4756851E-02 at 120iterations finished qdiffx linear iterations at : 06:28:33 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 2.8361040E-03 8.4756851E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 06:28:34 8.001u 0.205s 0:08.65 94.7% 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 06:28:34 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2025 !!! WARNING: SEP 194 has a net charge of -0.4750 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: 3.292773 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): -19.68700 23.83300 ymin,ymax (A): -40.36000 -0.6320001 zmin,zma (A): -36.93000 11.72200 x,y,z range (A): 43.52000 39.72800 48.65200 scale (grids/A): 3.292773 object centre (A): 2.073000 -20.49600 -12.60400 number of atom coordinates read : 2025 total number of charged atoms : 1897 net assigned charge : 6.025006 assigned positive charge : 307.6071 centred at (gu) : 89.71270 87.32626 94.94106 assigned negative charge : -301.5822 centred at (gu) : 88.92490 87.49480 95.35587 start vw surface at 0.1500000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 182807 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17003 grid for indexing accessible points = 1.400000 m= 103304 mr = 136556 m= 44801 mr = 86734 m= 14001 mr = 37276 m= 3087 mr = 10933 m= 420 mr = 2275 m= 18 mr = 291 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.040000 number of dielectric boundary points 74367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 15176 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) : 2.195182 object centre at (A) : 2.073000 -20.49600 -12.60400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2880484 6.2663108E-02 midg,1,midg; midg,igrid,midg 0.2707986 3.6353629E-02 1,midg,midg; igrid,midg,midg 0.3839057 0.3978647 gauss-seidel spectral radius is 0.9993094 estimated iterations to convergence 300 setup time was (sec) 2.350000 now iterating at: 06:28:36 rms-change max change #iterations 10.53406 445.3197 at 10iterations 6.269140 150.2033 at 20iterations 3.716325 68.36868 at 30iterations 2.209327 40.28716 at 40iterations 1.307217 22.96178 at 50iterations 0.7706664 13.19938 at 60iterations 0.4539583 7.854692 at 70iterations 0.2682919 4.747818 at 80iterations 0.1585419 2.737858 at 90iterations 9.3355134E-02 1.629669 at 100iterations 5.5231567E-02 0.9868841 at 110iterations 3.2754932E-02 0.5394936 at 120iterations 1.9651247E-02 0.3731308 at 130iterations 1.1971758E-02 0.2308521 at 140iterations 7.5158998E-03 0.1352921 at 150iterations 4.9253725E-03 8.4205627E-02 at 160iterations 3.3970322E-03 6.0661316E-02 at 170iterations 2.4941994E-03 4.3304443E-02 at 180iterations finished qdiffx linear iterations at : 06:28:46 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 2.4941994E-03 4.3304443E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 06:28:47 12.758u 0.184s 0:13.23 97.7% 0+0k 0+0io 0pf+0w