Sat Oct 15 14:18:00 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 14:18:00 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4763 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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: 0.5134344 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): -18.81700 36.48200 ymin,ymax (A): -30.58000 34.69300 zmin,zma (A): -3.878000 65.45900 x,y,z range (A): 55.29900 65.27300 69.33700 scale (grids/A): 0.5134344 object centre (A): 8.832501 2.056500 30.79050 number of atom coordinates read : 4763 total number of charged atoms : 4517 net assigned charge : 8.200027 assigned positive charge : 715.7525 centred at (gu) : 90.38985 90.52225 88.34319 assigned negative charge : -707.5569 centred at (gu) : 90.27639 90.54140 88.30193 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7815 nv = 96 ne = 84 npr = 97176 no. pairs analyzed = 97176 no. exposed pairs = 6049 no. arc points = 41978 no. surface atoms = 2024 nbur = 2739 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 = 1.652000 m= 296 mr = 3980 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4036 ## 584 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10451 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6169328E-11 1.6401959E-10 midg,1,midg; midg,igrid,midg 1.6434475E-10 8.7955157E-11 1,midg,midg; igrid,midg,midg -1.7972497E-10 5.0491811E-10 gauss-seidel spectral radius is 0.9805964 estimated iterations to convergence 59 setup time was (sec) 0.5800000 now iterating at: 14:18:01 rms-change max change #iterations 6.9335543E-02 9.751724 at 10iterations 4.5669647E-03 0.7376251 at 20iterations 8.4680557E-04 0.1083450 at 30iterations 3.1550718E-04 4.7029853E-02 at 40iterations 1.2248798E-04 1.9685030E-02 at 50iterations finished qdiffx linear iterations at : 14:18:04 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 1.2248798E-04 1.9685030E-02 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 14:18:04 4.155u 0.243s 0:04.72 93.0% 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 Sat Oct 15 2011 at 14:18:04 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 = 4763 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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: 1.540303 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): -18.81700 36.48200 ymin,ymax (A): -30.58000 34.69300 zmin,zma (A): -3.878000 65.45900 x,y,z range (A): 55.29900 65.27300 69.33700 scale (grids/A): 1.540303 object centre (A): 8.832501 2.056500 30.79050 number of atom coordinates read : 4763 total number of charged atoms : 4517 net assigned charge : 8.200027 assigned positive charge : 715.7525 centred at (gu) : 91.16838 91.56535 85.02824 assigned negative charge : -707.5569 centred at (gu) : 90.82908 91.62397 84.90589 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 88432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41978 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 24930 mr = 60349 m= 2165 mr = 16094 m= 46 mr = 891 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 0.4700000 number of dielectric boundary points 38239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 555 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 34004 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) : 0.5134344 object centre at (A) : 8.832501 2.056500 30.79050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0280335E-03 2.3228334E-02 midg,1,midg; midg,igrid,midg 4.2104610E-04 -8.6749336E-03 1,midg,midg; igrid,midg,midg -4.1415426E-04 1.3356680E-02 gauss-seidel spectral radius is 0.9981324 estimated iterations to convergence 184 setup time was (sec) 0.7500000 now iterating at: 14:18:05 rms-change max change #iterations 3.832950 155.2944 at 10iterations 1.572141 56.47243 at 20iterations 0.6514737 22.40346 at 30iterations 0.2678223 8.071353 at 40iterations 0.1104874 3.384468 at 50iterations 4.5904133E-02 1.664621 at 60iterations 1.8910252E-02 0.6438293 at 70iterations 7.8826146E-03 0.2507095 at 80iterations 3.3663143E-03 0.1119041 at 90iterations 1.4814264E-03 5.0775051E-02 at 100iterations 7.1555434E-04 2.2445679E-02 at 110iterations 3.9822294E-04 1.4043808E-02 at 120iterations finished qdiffx linear iterations at : 14:18:16 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 3.9822294E-04 1.4043808E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.500000 DelPhi exited at 14:18:16 9.504u 0.340s 0:11.70 84.1% 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 14:18:16 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 = 4763 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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: 2.310455 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): -18.81700 36.48200 ymin,ymax (A): -30.58000 34.69300 zmin,zma (A): -3.878000 65.45900 x,y,z range (A): 55.29900 65.27300 69.33700 scale (grids/A): 2.310455 object centre (A): 8.832501 2.056500 30.79050 number of atom coordinates read : 4763 total number of charged atoms : 4517 net assigned charge : 8.200027 assigned positive charge : 715.7525 centred at (gu) : 91.75227 92.34751 82.54205 assigned negative charge : -707.5569 centred at (gu) : 91.24352 92.43580 82.35891 start vw surface at 0.1300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 206163 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41978 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 89772 mr = 147997 m= 21976 mr = 69488 m= 3114 mr = 15355 m= 199 mr = 1879 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 352 time to turn everything in is 1.140000 number of dielectric boundary points 86440 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 36044 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) : 1.540303 object centre at (A) : 8.832501 2.056500 30.79050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1267259 0.5401813 midg,1,midg; midg,igrid,midg -0.1045856 -0.2492914 1,midg,midg; igrid,midg,midg 4.9308204E-04 0.2116434 gauss-seidel spectral radius is 0.9991693 estimated iterations to convergence 274 setup time was (sec) 1.430000 now iterating at: 14:18:18 rms-change max change #iterations 10.34630 337.6545 at 10iterations 5.961958 154.3522 at 20iterations 3.403086 80.06314 at 30iterations 1.931441 42.52312 at 40iterations 1.091456 22.42257 at 50iterations 0.6156874 12.55056 at 60iterations 0.3464760 6.904663 at 70iterations 0.1938769 4.169977 at 80iterations 0.1087732 2.162838 at 90iterations 6.0848523E-02 1.243099 at 100iterations 3.3971515E-02 0.6854852 at 110iterations 1.8975491E-02 0.3967247 at 120iterations 1.0582053E-02 0.2110176 at 130iterations 5.9221885E-03 0.1125259 at 140iterations 3.3073532E-03 6.8000793E-02 at 150iterations 1.8535445E-03 3.6735535E-02 at 160iterations 1.0428400E-03 2.4456024E-02 at 170iterations 5.9468305E-04 1.1417866E-02 at 180iterations finished qdiffx linear iterations at : 14:18:34 total time elapsed so far: 15.55000 # loops : 180 mean,max change (kT/e) : 5.9468305E-04 1.1417866E-02 energy calculations done at 15.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.67000 DelPhi exited at 14:18:34 15.676u 0.311s 0:17.86 89.4% 0+0k 0+0io 0pf+0w