Sat Oct 8 16:25:35 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 8 2011 at 16:25:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2286 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: 0.6615871 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): -1.935000 47.62700 ymin,ymax (A): -16.25900 29.16900 zmin,zma (A): -17.44200 36.36800 x,y,z range (A): 49.56200 45.42800 53.81000 scale (grids/A): 0.6615871 object centre (A): 22.84600 6.454999 9.463000 number of atom coordinates read : 2286 total number of charged atoms : 2227 net assigned charge : 4.000001 assigned positive charge : 341.8282 centred at (gu) : 89.97356 88.83813 89.85247 assigned negative charge : -337.8288 centred at (gu) : 90.00942 88.93819 89.89291 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6767 nv = 96 ne = 84 npr = 45708 no. pairs analyzed = 45708 no. exposed pairs = 2948 no. arc points = 20389 no. surface atoms = 1011 nbur = 1275 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 3726 m= 4 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3500000 number of dielectric boundary points 3409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1942 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8125 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8122041E-08 3.0096594E-09 midg,1,midg; midg,igrid,midg 3.5837427E-08 -5.9622334E-09 1,midg,midg; igrid,midg,midg 1.6860648E-08 3.8939589E-09 gauss-seidel spectral radius is 0.9881321 estimated iterations to convergence 75 setup time was (sec) 0.6600000 now iterating at: 16:25:37 rms-change max change #iterations 0.1527147 24.59354 at 10iterations 1.6611055E-02 2.346124 at 20iterations 1.7622068E-03 0.2543392 at 30iterations 2.0573066E-04 2.8364182E-02 at 40iterations 3.2029053E-05 5.4132938E-03 at 50iterations finished qdiffx linear iterations at : 16:25:40 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 3.2029053E-05 5.4132938E-03 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 16:25:41 4.407u 0.436s 0:05.12 94.3% 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 8 2011 at 16:25:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2286 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: 1.984761 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): -1.935000 47.62700 ymin,ymax (A): -16.25900 29.16900 zmin,zma (A): -17.44200 36.36800 x,y,z range (A): 49.56200 45.42800 53.81000 scale (grids/A): 1.984761 object centre (A): 22.84600 6.454999 9.463000 number of atom coordinates read : 2286 total number of charged atoms : 2227 net assigned charge : 4.000001 assigned positive charge : 341.8282 centred at (gu) : 89.92001 86.51386 89.55692 assigned negative charge : -337.8288 centred at (gu) : 90.02828 86.81450 89.67863 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 72538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20389 grid for indexing accessible points = 1.400000 m= 27197 mr = 50253 m= 5202 mr = 20099 m= 387 mr = 3450 m= 5 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1215 time to turn everything in is 0.7700000 number of dielectric boundary points 31360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 17611 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) : 0.6615871 object centre at (A) : 22.84600 6.454999 9.463000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2807998E-02 -8.3415927E-03 midg,1,midg; midg,igrid,midg 2.1794578E-02 -3.6112363E-03 1,midg,midg; igrid,midg,midg 7.0446995E-03 -3.3632413E-02 gauss-seidel spectral radius is 0.9987096 estimated iterations to convergence 221 setup time was (sec) 1.090000 now iterating at: 16:25:42 rms-change max change #iterations 4.262621 153.3172 at 10iterations 2.032271 79.08147 at 20iterations 0.9710945 31.38767 at 30iterations 0.4656190 14.78597 at 40iterations 0.2227189 7.072088 at 50iterations 0.1070534 3.465714 at 60iterations 5.1198356E-02 1.651768 at 70iterations 2.4516746E-02 0.7693925 at 80iterations 1.1737645E-02 0.3517227 at 90iterations 5.6186793E-03 0.1780396 at 100iterations 2.6940543E-03 8.2345963E-02 at 110iterations 1.2954531E-03 4.3222427E-02 at 120iterations finished qdiffx linear iterations at : 16:25:51 total time elapsed so far: 10.18000 # loops : 120 mean,max change (kT/e) : 1.2954531E-03 4.3222427E-02 energy calculations done at 10.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.39000 DelPhi exited at 16:25:52 10.390u 0.481s 0:11.38 95.5% 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 8 2011 at 16:25:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2286 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: 2.977142 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): -1.935000 47.62700 ymin,ymax (A): -16.25900 29.16900 zmin,zma (A): -17.44200 36.36800 x,y,z range (A): 49.56200 45.42800 53.81000 scale (grids/A): 2.977142 object centre (A): 22.84600 6.454999 9.463000 number of atom coordinates read : 2286 total number of charged atoms : 2227 net assigned charge : 4.000001 assigned positive charge : 341.8282 centred at (gu) : 89.87992 84.77060 89.33530 assigned negative charge : -337.8288 centred at (gu) : 90.04222 85.22173 89.51784 start vw surface at 0.1500000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 167939 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20389 grid for indexing accessible points = 1.400000 m= 85442 mr = 122050 m= 33776 mr = 69674 m= 9790 mr = 27490 m= 1728 mr = 7592 m= 143 mr = 1205 m= 5 mr = 85 m= 0 mr = 2 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 3955 time to turn everything in is 2.030000 number of dielectric boundary points 70725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 17816 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) : 1.984761 object centre at (A) : 22.84600 6.454999 9.463000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3525818 -0.1794424 midg,1,midg; midg,igrid,midg 0.1563556 -6.2474012E-02 1,midg,midg; igrid,midg,midg 5.1362973E-02 -0.4678947 gauss-seidel spectral radius is 0.9992789 estimated iterations to convergence 294 setup time was (sec) 2.380000 now iterating at: 16:25:55 rms-change max change #iterations 9.876806 370.4144 at 10iterations 5.828566 161.2255 at 20iterations 3.435153 74.15432 at 30iterations 2.018033 40.67884 at 40iterations 1.179345 22.13678 at 50iterations 0.6889418 13.33038 at 60iterations 0.4014623 7.535695 at 70iterations 0.2342707 4.002100 at 80iterations 0.1363251 2.515545 at 90iterations 7.8982875E-02 1.450408 at 100iterations 4.5820203E-02 0.8260603 at 110iterations 2.6655752E-02 0.4731045 at 120iterations 1.5482668E-02 0.2815342 at 130iterations 8.9654634E-03 0.1533432 at 140iterations 5.2089822E-03 9.6893311E-02 at 150iterations 3.0286959E-03 5.4709435E-02 at 160iterations 1.7665375E-03 3.1822205E-02 at 170iterations 1.0356067E-03 2.1820068E-02 at 180iterations finished qdiffx linear iterations at : 16:26:10 total time elapsed so far: 17.50000 # loops : 180 mean,max change (kT/e) : 1.0356067E-03 2.1820068E-02 energy calculations done at 17.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.73000 DelPhi exited at 16:26:11 17.735u 0.527s 0:18.53 98.4% 0+0k 0+0io 0pf+0w