Mon Oct 10 09:15:09 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 Mon Oct 10 2011 at 09:15:09 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6469551 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): -6.219000 34.36600 ymin,ymax (A): -3.437000 49.21900 zmin,zma (A): -24.11500 30.91200 x,y,z range (A): 40.58500 52.65600 55.02700 scale (grids/A): 0.6469551 object centre (A): 14.07350 22.89100 3.398500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 90.87991 92.24431 90.21267 assigned negative charge : -288.8262 centred at (gu) : 91.00053 92.36975 90.15275 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5630 nv = 96 ne = 84 npr = 40181 no. pairs analyzed = 40181 no. exposed pairs = 2453 no. arc points = 17419 no. surface atoms = 831 nbur = 1133 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 287 mr = 3112 m= 0 mr = 38 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1750 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6565 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8643206E-10 1.2482639E-08 midg,1,midg; midg,igrid,midg 1.1621708E-08 -1.2461971E-08 1,midg,midg; igrid,midg,midg 1.5044687E-08 -8.4907565E-09 gauss-seidel spectral radius is 0.9875645 estimated iterations to convergence 73 setup time was (sec) 0.4600000 now iterating at: 09:15:10 rms-change max change #iterations 0.1350830 22.83216 at 10iterations 1.3582623E-02 2.204720 at 20iterations 1.3781196E-03 0.2191420 at 30iterations 1.3819159E-04 1.9763947E-02 at 40iterations 1.4120335E-05 2.5024414E-03 at 50iterations finished qdiffx linear iterations at : 09:15:12 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 1.4120335E-05 2.5024414E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 09:15:13 3.102u 0.153s 0:03.65 89.0% 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 Mon Oct 10 2011 at 09:15:13 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.940865 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): -6.219000 34.36600 ymin,ymax (A): -3.437000 49.21900 zmin,zma (A): -24.11500 30.91200 x,y,z range (A): 40.58500 52.65600 55.02700 scale (grids/A): 1.940865 object centre (A): 14.07350 22.89100 3.398500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 92.63953 96.73265 90.63804 assigned negative charge : -288.8262 centred at (gu) : 93.00164 97.10942 90.45826 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 60445 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17419 grid for indexing accessible points = 1.400000 m= 22034 mr = 41564 m= 3541 mr = 16791 m= 205 mr = 2411 m= 1 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2668 time to turn everything in is 0.4300000 number of dielectric boundary points 25378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 14456 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) : 0.6469551 object centre at (A) : 14.07350 22.89100 3.398500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4880494E-02 1.6532853E-02 midg,1,midg; midg,igrid,midg 3.3347078E-02 -7.5167804E-03 1,midg,midg; igrid,midg,midg 7.1027172E-03 -5.6400462E-03 gauss-seidel spectral radius is 0.9986082 estimated iterations to convergence 212 setup time was (sec) 0.6800000 now iterating at: 09:15:14 rms-change max change #iterations 3.761864 173.7291 at 10iterations 1.744716 73.83670 at 20iterations 0.8128787 29.60617 at 30iterations 0.3790951 14.12731 at 40iterations 0.1750647 6.099865 at 50iterations 8.1016131E-02 3.084150 at 60iterations 3.7789572E-02 1.259521 at 70iterations 1.7555770E-02 0.5989370 at 80iterations 8.1683183E-03 0.2982502 at 90iterations 3.7871778E-03 0.1225481 at 100iterations 1.7529936E-03 6.3362122E-02 at 110iterations 8.2036969E-04 2.6123643E-02 at 120iterations finished qdiffx linear iterations at : 09:15:20 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 8.2036969E-04 2.6123643E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.910000 DelPhi exited at 09:15:20 6.917u 0.192s 0:07.41 95.8% 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 Mon Oct 10 2011 at 09:15:20 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.911298 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): -6.219000 34.36600 ymin,ymax (A): -3.437000 49.21900 zmin,zma (A): -24.11500 30.91200 x,y,z range (A): 40.58500 52.65600 55.02700 scale (grids/A): 2.911298 object centre (A): 14.07350 22.89100 3.398500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 93.95923 100.0989 90.95711 assigned negative charge : -288.8262 centred at (gu) : 94.50247 100.6641 90.68749 start vw surface at 0.1400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 139315 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17419 grid for indexing accessible points = 1.400000 m= 70639 mr = 100061 m= 26401 mr = 58653 m= 6361 mr = 22051 m= 890 mr = 5092 m= 29 mr = 646 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.5899999 no. cavity mid-points inaccessible to solvent = 8921 time to turn everything in is 1.070000 number of dielectric boundary points 57118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 14656 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) : 1.940865 object centre at (A) : 14.07350 22.89100 3.398500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.081379 3.6442261E-02 midg,1,midg; midg,igrid,midg 0.3100607 -0.1136758 1,midg,midg; igrid,midg,midg 3.6701836E-02 -3.2567095E-02 gauss-seidel spectral radius is 0.9992384 estimated iterations to convergence 286 setup time was (sec) 1.350000 now iterating at: 09:15:22 rms-change max change #iterations 8.727529 361.8456 at 10iterations 4.986366 129.0744 at 20iterations 2.843533 66.07565 at 30iterations 1.616959 39.64708 at 40iterations 0.9230018 17.56580 at 50iterations 0.5254923 11.32941 at 60iterations 0.2985347 6.208324 at 70iterations 0.1699553 3.522497 at 80iterations 9.6496403E-02 1.876843 at 90iterations 5.4876834E-02 1.073198 at 100iterations 3.1227337E-02 0.6201458 at 110iterations 1.7748291E-02 0.3453703 at 120iterations 1.0090658E-02 0.1925169 at 130iterations 5.7357010E-03 0.1147871 at 140iterations 3.2704014E-03 6.0127258E-02 at 150iterations 1.8563283E-03 3.5301208E-02 at 160iterations 1.0560952E-03 2.0369530E-02 at 170iterations 6.0065935E-04 1.2336731E-02 at 180iterations finished qdiffx linear iterations at : 09:15:31 total time elapsed so far: 10.81000 # loops : 180 mean,max change (kT/e) : 6.0065935E-04 1.2336731E-02 energy calculations done at 10.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.98000 DelPhi exited at 09:15:32 10.982u 0.206s 0:11.55 96.7% 0+0k 0+0io 0pf+0w