Tue Oct 11 06:55:36 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 06:55:36 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2956 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 0.5358621 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): -20.07400 46.36100 ymin,ymax (A): 21.90000 77.49000 zmin,zma (A): -72.41800 -23.01600 x,y,z range (A): 66.43500 55.59000 49.40200 scale (grids/A): 0.5358621 object centre (A): 13.14350 49.69500 -47.71700 number of atom coordinates read : 2956 total number of charged atoms : 2814 net assigned charge : -2.960991 assigned positive charge : 432.8105 centred at (gu) : 89.09137 90.06063 89.83937 assigned negative charge : -435.7722 centred at (gu) : 89.07154 90.15395 89.85358 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5426 nv = 96 ne = 84 npr = 61132 no. pairs analyzed = 61132 no. exposed pairs = 3699 no. arc points = 26071 no. surface atoms = 1249 nbur = 1707 mkacc time = 0.1700000 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= 202 mr = 2795 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 2824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2643 ## 351 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7236 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1294372E-11 -1.7766681E-10 midg,1,midg; midg,igrid,midg 2.8208155E-10 -5.4856258E-10 1,midg,midg; igrid,midg,midg -2.6361383E-10 -2.8215768E-11 gauss-seidel spectral radius is 0.9820510 estimated iterations to convergence 62 setup time was (sec) 0.6600000 now iterating at: 06:55:37 rms-change max change #iterations 6.6943951E-02 11.25733 at 10iterations 4.1684550E-03 0.6597786 at 20iterations 2.6392966E-04 4.8431396E-02 at 30iterations 1.6931781E-05 3.2291412E-03 at 40iterations 1.1021887E-06 1.7881393E-04 at 50iterations finished qdiffx linear iterations at : 06:55:40 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 1.1021887E-06 1.7881393E-04 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 06:55:41 4.242u 0.281s 0:05.01 90.2% 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 06:55:41 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2956 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 1.607586 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): -20.07400 46.36100 ymin,ymax (A): 21.90000 77.49000 zmin,zma (A): -72.41800 -23.01600 x,y,z range (A): 66.43500 55.59000 49.40200 scale (grids/A): 1.607586 object centre (A): 13.14350 49.69500 -47.71700 number of atom coordinates read : 2956 total number of charged atoms : 2814 net assigned charge : -2.960991 assigned positive charge : 432.8105 centred at (gu) : 87.27395 90.18130 89.51740 assigned negative charge : -435.7722 centred at (gu) : 87.21426 90.46156 89.56026 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 60387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26071 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18322 mr = 40732 m= 1834 mr = 12730 m= 49 mr = 937 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 26193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 309 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 21482 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) : 0.5358621 object centre at (A) : 13.14350 49.69500 -47.71700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8556215E-03 7.0294086E-03 midg,1,midg; midg,igrid,midg -4.3877647E-03 3.1513508E-04 1,midg,midg; igrid,midg,midg -2.8770317E-03 -1.9527847E-02 gauss-seidel spectral radius is 0.9981233 estimated iterations to convergence 183 setup time was (sec) 0.8700000 now iterating at: 06:55:42 rms-change max change #iterations 3.182951 140.9671 at 10iterations 1.301803 49.69914 at 20iterations 0.5355889 20.57215 at 30iterations 0.2199406 9.590162 at 40iterations 9.0739973E-02 3.528962 at 50iterations 3.7195072E-02 1.519887 at 60iterations 1.5287933E-02 0.5848980 at 70iterations 6.2889191E-03 0.2549057 at 80iterations 2.5823773E-03 0.1079967 at 90iterations 1.0630161E-03 3.8581848E-02 at 100iterations 4.3942270E-04 1.5595436E-02 at 110iterations 1.7999340E-04 6.5994263E-03 at 120iterations finished qdiffx linear iterations at : 06:55:51 total time elapsed so far: 9.120000 # loops : 120 mean,max change (kT/e) : 1.7999340E-04 6.5994263E-03 energy calculations done at 9.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.310000 DelPhi exited at 06:55:51 9.309u 0.297s 0:09.91 96.7% 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 06:55:51 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2956 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 2.411380 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): -20.07400 46.36100 ymin,ymax (A): 21.90000 77.49000 zmin,zma (A): -72.41800 -23.01600 x,y,z range (A): 66.43500 55.59000 49.40200 scale (grids/A): 2.411380 object centre (A): 13.14350 49.69500 -47.71700 number of atom coordinates read : 2956 total number of charged atoms : 2814 net assigned charge : -2.960991 assigned positive charge : 432.8105 centred at (gu) : 85.91077 90.27185 89.27586 assigned negative charge : -435.7722 centred at (gu) : 85.82136 90.69236 89.34024 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 140296 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26071 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 63783 mr = 99669 m= 18108 mr = 50617 m= 2785 mr = 13726 m= 195 mr = 1911 m= 2 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 59164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 22483 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) : 1.607586 object centre at (A) : 13.14350 49.69500 -47.71700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3262953E-02 0.1385105 midg,1,midg; midg,igrid,midg -7.2921328E-02 2.6936583E-02 1,midg,midg; igrid,midg,midg -0.1103730 -0.3841220 gauss-seidel spectral radius is 0.9991178 estimated iterations to convergence 266 setup time was (sec) 1.640000 now iterating at: 06:55:53 rms-change max change #iterations 8.223179 302.9681 at 10iterations 4.566263 132.1842 at 20iterations 2.529228 63.02435 at 30iterations 1.389980 30.34184 at 40iterations 0.7639662 18.43633 at 50iterations 0.4184248 9.280699 at 60iterations 0.2294883 5.544528 at 70iterations 0.1253575 2.895373 at 80iterations 6.8497226E-02 1.472889 at 90iterations 3.7390575E-02 0.7279024 at 100iterations 2.0406010E-02 0.4236221 at 110iterations 1.1118461E-02 0.2383060 at 120iterations 6.0770693E-03 0.1290662 at 130iterations 3.3153729E-03 6.9921017E-02 at 140iterations 1.8057062E-03 4.3291569E-02 at 150iterations 9.8569714E-04 2.0326614E-02 at 160iterations 5.3713447E-04 1.2413979E-02 at 170iterations 2.9194431E-04 6.0868263E-03 at 180iterations finished qdiffx linear iterations at : 06:56:07 total time elapsed so far: 15.08000 # loops : 180 mean,max change (kT/e) : 2.9194431E-04 6.0868263E-03 energy calculations done at 15.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.25000 DelPhi exited at 06:56:07 15.255u 0.345s 0:16.10 96.8% 0+0k 0+0io 0pf+0w