Tue Oct 11 06:13:19 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 06:13:19 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2228 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: 0.7019620 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): 16.92600 63.99500 ymin,ymax (A): -3.562000 33.43900 zmin,zma (A): 19.27600 69.99100 x,y,z range (A): 47.06900 37.00100 50.71500 scale (grids/A): 0.7019620 object centre (A): 40.46050 14.93850 44.63350 number of atom coordinates read : 2228 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.5790 centred at (gu) : 90.64140 89.74797 89.84998 assigned negative charge : -305.0792 centred at (gu) : 90.77371 89.77888 89.80248 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6820 nv = 96 ne = 84 npr = 40788 no. pairs analyzed = 40788 no. exposed pairs = 2469 no. arc points = 16843 no. surface atoms = 835 nbur = 1393 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 3889 m= 5 mr = 74 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 0.2800000 number of dielectric boundary points 3266 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1517 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7566 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8954245E-08 6.6824171E-08 midg,1,midg; midg,igrid,midg 6.4811083E-08 3.3720308E-08 1,midg,midg; igrid,midg,midg 9.2124523E-08 -1.0369634E-08 gauss-seidel spectral radius is 0.9894180 estimated iterations to convergence 79 setup time was (sec) 0.5400000 now iterating at: 06:13:19 rms-change max change #iterations 0.1906582 26.54176 at 10iterations 2.3335641E-02 2.887088 at 20iterations 3.0370681E-03 0.3967953 at 30iterations 4.5710764E-04 5.8937073E-02 at 40iterations 9.2903523E-05 1.1949539E-02 at 50iterations finished qdiffx linear iterations at : 06:13:22 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 9.2903523E-05 1.1949539E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 06:13:23 3.518u 0.181s 0:04.19 88.0% 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 Tue Oct 11 2011 at 06:13:23 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2228 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: 2.105886 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): 16.92600 63.99500 ymin,ymax (A): -3.562000 33.43900 zmin,zma (A): 19.27600 69.99100 x,y,z range (A): 47.06900 37.00100 50.71500 scale (grids/A): 2.105886 object centre (A): 40.46050 14.93850 44.63350 number of atom coordinates read : 2228 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.5790 centred at (gu) : 91.92424 89.24391 89.54978 assigned negative charge : -305.0792 centred at (gu) : 92.32137 89.33680 89.40762 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 72600 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16843 grid for indexing accessible points = 1.400000 m= 28405 mr = 51638 m= 5209 mr = 21447 m= 484 mr = 3433 m= 10 mr = 275 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 29915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15175 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) : 0.7019620 object centre at (A) : 40.46050 14.93850 44.63350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4919661E-02 5.1935054E-02 midg,1,midg; midg,igrid,midg 2.6897801E-02 1.2357506E-02 1,midg,midg; igrid,midg,midg 3.0594576E-02 1.9458063E-02 gauss-seidel spectral radius is 0.9988112 estimated iterations to convergence 230 setup time was (sec) 0.8800000 now iterating at: 06:13:24 rms-change max change #iterations 4.481899 277.1389 at 10iterations 2.212809 88.69305 at 20iterations 1.085894 37.57618 at 30iterations 0.5392705 16.77017 at 40iterations 0.2661802 8.277493 at 50iterations 0.1316990 4.147444 at 60iterations 6.4947717E-02 1.991913 at 70iterations 3.2153159E-02 1.057346 at 80iterations 1.5906692E-02 0.5093079 at 90iterations 7.8899423E-03 0.2503009 at 100iterations 3.9516436E-03 0.1209183 at 110iterations 1.9896408E-03 5.9989929E-02 at 120iterations finished qdiffx linear iterations at : 06:13:31 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.9896408E-03 5.9989929E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 06:13:31 7.931u 0.226s 0:08.63 94.4% 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 Tue Oct 11 2011 at 06:13:32 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2228 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: 3.158829 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): 16.92600 63.99500 ymin,ymax (A): -3.562000 33.43900 zmin,zma (A): 19.27600 69.99100 x,y,z range (A): 47.06900 37.00100 50.71500 scale (grids/A): 3.158829 object centre (A): 40.46050 14.93850 44.63350 number of atom coordinates read : 2228 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.5790 centred at (gu) : 92.88635 88.86584 89.32468 assigned negative charge : -305.0792 centred at (gu) : 93.48216 89.00521 89.11146 start vw surface at 0.1400000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 167404 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16843 grid for indexing accessible points = 1.400000 m= 89446 mr = 124314 m= 35402 mr = 74444 m= 9809 mr = 28915 m= 1966 mr = 7581 m= 242 mr = 1467 m= 3 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.800000 number of dielectric boundary points 67401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 15399 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) : 2.105886 object centre at (A) : 40.46050 14.93850 44.63350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2828636 0.3781476 midg,1,midg; midg,igrid,midg 0.2345727 0.1027110 1,midg,midg; igrid,midg,midg 0.2508247 0.3417367 gauss-seidel spectral radius is 0.9992892 estimated iterations to convergence 296 setup time was (sec) 2.130000 now iterating at: 06:13:34 rms-change max change #iterations 9.981062 324.8732 at 10iterations 5.865042 127.0704 at 20iterations 3.439158 63.93254 at 30iterations 2.022292 45.03381 at 40iterations 1.182182 22.28329 at 50iterations 0.6916903 13.39645 at 60iterations 0.4032591 7.723782 at 70iterations 0.2361700 4.461338 at 80iterations 0.1375797 2.423367 at 90iterations 8.0373995E-02 1.434135 at 100iterations 4.7058292E-02 0.8199463 at 110iterations 2.7582295E-02 0.4645844 at 120iterations 1.6315356E-02 0.3033829 at 130iterations 9.7213928E-03 0.1736832 at 140iterations 5.9295520E-03 0.1168861 at 150iterations 3.7072159E-03 6.8973541E-02 at 160iterations 2.4433862E-03 4.8316956E-02 at 170iterations 1.6951129E-03 3.4992218E-02 at 180iterations finished qdiffx linear iterations at : 06:13:45 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 1.6951129E-03 3.4992218E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 06:13:45 13.088u 0.217s 0:13.74 96.7% 0+0k 0+0io 0pf+0w