Sat Oct 15 14:05:31 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 Sat Oct 15 2011 at 14:05:31 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4724 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5097001 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): -18.08300 37.01600 ymin,ymax (A): -30.57400 34.27900 zmin,zma (A): -3.936000 65.90900 x,y,z range (A): 55.09900 64.85300 69.84500 scale (grids/A): 0.5097001 object centre (A): 9.466501 1.852501 30.98650 number of atom coordinates read : 4724 total number of charged atoms : 4478 net assigned charge : 6.800033 assigned positive charge : 708.8535 centred at (gu) : 90.04394 90.49534 88.18543 assigned negative charge : -702.0579 centred at (gu) : 89.92563 90.55836 88.17684 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7851 nv = 96 ne = 84 npr = 94617 no. pairs analyzed = 94617 no. exposed pairs = 6073 no. arc points = 42320 no. surface atoms = 2037 nbur = 2687 mkacc time = 0.1600000 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 = 1.680000 m= 289 mr = 4003 m= 2 mr = 8 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 0.3100000 number of dielectric boundary points 4131 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4043 ## 573 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10362 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1555656E-10 7.2033469E-11 midg,1,midg; midg,igrid,midg 2.1627261E-10 -7.1048424E-11 1,midg,midg; igrid,midg,midg -1.9764063E-10 3.8260237E-10 gauss-seidel spectral radius is 0.9803167 estimated iterations to convergence 59 setup time was (sec) 0.5300000 now iterating at: 14:05:32 rms-change max change #iterations 6.6373572E-02 9.805645 at 10iterations 3.9990889E-03 0.6320934 at 20iterations 5.5607513E-04 8.3097458E-02 at 30iterations 2.0464759E-04 2.7701974E-02 at 40iterations 8.2417202E-05 1.1355639E-02 at 50iterations finished qdiffx linear iterations at : 14:05:35 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 8.2417202E-05 1.1355639E-02 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 14:05:36 3.768u 0.210s 0:04.32 91.8% 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 Sat Oct 15 2011 at 14:05:36 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4724 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.529100 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): -18.08300 37.01600 ymin,ymax (A): -30.57400 34.27900 zmin,zma (A): -3.936000 65.90900 x,y,z range (A): 55.09900 64.85300 69.84500 scale (grids/A): 1.529100 object centre (A): 9.466501 1.852501 30.98650 number of atom coordinates read : 4724 total number of charged atoms : 4478 net assigned charge : 6.800033 assigned positive charge : 708.8535 centred at (gu) : 90.13062 91.48462 84.55453 assigned negative charge : -702.0579 centred at (gu) : 89.77663 91.67488 84.53030 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 88972 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42320 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26184 mr = 60759 m= 2327 mr = 17304 m= 64 mr = 982 m= 0 mr = 5 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 38497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 536 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 33619 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) : 0.5097001 object centre at (A) : 9.466501 1.852501 30.98650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4426005E-03 1.8569637E-02 midg,1,midg; midg,igrid,midg 1.0070885E-02 -1.2026148E-02 1,midg,midg; igrid,midg,midg -1.9032067E-03 1.1520159E-02 gauss-seidel spectral radius is 0.9981068 estimated iterations to convergence 183 setup time was (sec) 0.6700000 now iterating at: 14:05:37 rms-change max change #iterations 3.762414 144.2525 at 10iterations 1.538801 50.61453 at 20iterations 0.6313019 19.99169 at 30iterations 0.2592825 7.710472 at 40iterations 0.1058240 3.564254 at 50iterations 4.3712087E-02 1.426673 at 60iterations 1.7889861E-02 0.6257696 at 70iterations 7.3860348E-03 0.2704315 at 80iterations 3.0834470E-03 0.1144104 at 90iterations 1.3137839E-03 4.6698570E-02 at 100iterations 5.9601519E-04 2.2064209E-02 at 110iterations 3.0555061E-04 1.0200500E-02 at 120iterations finished qdiffx linear iterations at : 14:05:44 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 3.0555061E-04 1.0200500E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 14:05:45 8.183u 0.215s 0:09.15 91.6% 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 Sat Oct 15 2011 at 14:05:45 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4724 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.293650 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): -18.08300 37.01600 ymin,ymax (A): -30.57400 34.27900 zmin,zma (A): -3.936000 65.90900 x,y,z range (A): 55.09900 64.85300 69.84500 scale (grids/A): 2.293650 object centre (A): 9.466501 1.852501 30.98650 number of atom coordinates read : 4724 total number of charged atoms : 4478 net assigned charge : 6.800033 assigned positive charge : 708.8535 centred at (gu) : 90.19543 92.22680 81.83156 assigned negative charge : -702.0579 centred at (gu) : 89.66496 92.51210 81.79541 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 207216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42320 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 93664 mr = 149306 m= 23947 mr = 72882 m= 3400 mr = 17115 m= 207 mr = 2031 m= 0 mr = 71 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 87029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 35727 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) : 1.529100 object centre at (A) : 9.466501 1.852501 30.98650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1315621 0.4448789 midg,1,midg; midg,igrid,midg 0.1809738 -0.3128365 1,midg,midg; igrid,midg,midg -1.7087465E-02 0.1714199 gauss-seidel spectral radius is 0.9991627 estimated iterations to convergence 273 setup time was (sec) 1.370000 now iterating at: 14:05:46 rms-change max change #iterations 10.18464 295.8949 at 10iterations 5.857934 143.5518 at 20iterations 3.340446 71.45567 at 30iterations 1.891327 39.98137 at 40iterations 1.067205 22.92104 at 50iterations 0.5991312 12.43795 at 60iterations 0.3363847 6.513931 at 70iterations 0.1884375 3.705329 at 80iterations 0.1054760 2.211381 at 90iterations 5.8722306E-02 1.204964 at 100iterations 3.2701939E-02 0.6132469 at 110iterations 1.8235764E-02 0.3797646 at 120iterations 1.0182516E-02 0.2034802 at 130iterations 5.6863758E-03 0.1079946 at 140iterations 3.1825677E-03 6.6917419E-02 at 150iterations 1.7968017E-03 3.4669876E-02 at 160iterations 1.0309647E-03 2.2495747E-02 at 170iterations 6.0856814E-04 1.4425278E-02 at 180iterations finished qdiffx linear iterations at : 14:06:01 total time elapsed so far: 14.02000 # loops : 180 mean,max change (kT/e) : 6.0856814E-04 1.4425278E-02 energy calculations done at 14.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.15000 DelPhi exited at 14:06:02 14.147u 0.264s 0:17.02 84.6% 0+0k 0+0io 0pf+0w