Mon Oct 10 19:34:00 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 Mon Oct 10 2011 at 19:34:00 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2946 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6253183 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): -37.43500 18.99300 ymin,ymax (A): -36.88800 20.04300 zmin,zma (A): -27.59000 24.81000 x,y,z range (A): 56.42800 56.93100 52.40000 scale (grids/A): 0.6253183 object centre (A): -9.220999 -8.422501 -1.390000 number of atom coordinates read : 2946 total number of charged atoms : 2804 net assigned charge : 3.000013 assigned positive charge : 440.7954 centred at (gu) : 87.34263 90.44384 89.45872 assigned negative charge : -437.7967 centred at (gu) : 87.27503 90.57323 89.45516 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7939 nv = 96 ne = 84 npr = 56145 no. pairs analyzed = 56145 no. exposed pairs = 4206 no. arc points = 30547 no. surface atoms = 1410 nbur = 1536 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 446 mr = 3760 m= 2 mr = 28 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 0.4600000 number of dielectric boundary points 4599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3001 ## 285 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 9514 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0806486E-09 2.9982010E-09 midg,1,midg; midg,igrid,midg 1.2788440E-08 -9.1939363E-09 1,midg,midg; igrid,midg,midg -5.3543294E-09 4.9994977E-09 gauss-seidel spectral radius is 0.9868077 estimated iterations to convergence 71 setup time was (sec) 0.8000000 now iterating at: 19:34:01 rms-change max change #iterations 0.1393223 21.36006 at 10iterations 1.2970051E-02 2.073479 at 20iterations 1.2651085E-03 0.1859570 at 30iterations 1.6329651E-04 2.3836136E-02 at 40iterations 4.3404601E-05 6.4356327E-03 at 50iterations finished qdiffx linear iterations at : 19:34:05 total time elapsed so far: 4.610000 # loops : 50 mean,max change (kT/e) : 4.3404601E-05 6.4356327E-03 energy calculations done at 4.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.830000 DelPhi exited at 19:34:06 4.834u 0.382s 0:05.99 86.9% 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 19:34:06 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2946 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.875955 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): -37.43500 18.99300 ymin,ymax (A): -36.88800 20.04300 zmin,zma (A): -27.59000 24.81000 x,y,z range (A): 56.42800 56.93100 52.40000 scale (grids/A): 1.875955 object centre (A): -9.220999 -8.422501 -1.390000 number of atom coordinates read : 2946 total number of charged atoms : 2804 net assigned charge : 3.000013 assigned positive charge : 440.7954 centred at (gu) : 82.02721 91.33094 88.37518 assigned negative charge : -437.7967 centred at (gu) : 81.82516 91.71944 88.36552 start vw surface at 0.1700000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 83776 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30547 grid for indexing accessible points = 1.400000 m= 28468 mr = 52741 m= 4917 mr = 19394 m= 270 mr = 2679 m= 7 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8800000 number of dielectric boundary points 42575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 159 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 22032 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) : 0.6253183 object centre at (A) : -9.220999 -8.422501 -1.390000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9692864E-02 2.3908781E-02 midg,1,midg; midg,igrid,midg 2.2710266E-02 -5.7094442E-03 1,midg,midg; igrid,midg,midg -3.3999651E-03 6.0946061E-03 gauss-seidel spectral radius is 0.9986632 estimated iterations to convergence 217 setup time was (sec) 1.230000 now iterating at: 19:34:07 rms-change max change #iterations 4.460355 171.7028 at 10iterations 2.091140 71.29988 at 20iterations 0.9844072 34.09985 at 30iterations 0.4635695 16.29045 at 40iterations 0.2179345 6.211826 at 50iterations 0.1029391 3.177308 at 60iterations 4.8307948E-02 1.583107 at 70iterations 2.2778064E-02 0.6635714 at 80iterations 1.0748112E-02 0.3749008 at 90iterations 5.0861929E-03 0.1659279 at 100iterations 2.4053422E-03 7.6469183E-02 at 110iterations 1.1499994E-03 3.3802986E-02 at 120iterations finished qdiffx linear iterations at : 19:34:18 total time elapsed so far: 11.60000 # loops : 120 mean,max change (kT/e) : 1.1499994E-03 3.3802986E-02 energy calculations done at 11.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.83000 DelPhi exited at 19:34:18 11.834u 0.471s 0:12.64 97.3% 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 Mon Oct 10 2011 at 19:34:19 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2946 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.813933 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): -37.43500 18.99300 ymin,ymax (A): -36.88800 20.04300 zmin,zma (A): -27.59000 24.81000 x,y,z range (A): 56.42800 56.93100 52.40000 scale (grids/A): 2.813933 object centre (A): -9.220999 -8.422501 -1.390000 number of atom coordinates read : 2946 total number of charged atoms : 2804 net assigned charge : 3.000013 assigned positive charge : 440.7954 centred at (gu) : 78.04065 91.99631 87.56250 assigned negative charge : -437.7967 centred at (gu) : 77.73756 92.57923 87.54822 start vw surface at 0.1600000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 193185 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30547 grid for indexing accessible points = 1.400000 m= 90536 mr = 129451 m= 33948 mr = 69588 m= 8597 mr = 25865 m= 1075 mr = 5889 m= 49 mr = 542 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 1.390000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.260000 number of dielectric boundary points 96048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.440000 number of grid points assigned charge 22426 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) : 1.875955 object centre at (A) : -9.220999 -8.422501 -1.390000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2954070 0.3940700 midg,1,midg; midg,igrid,midg 0.4717789 -4.1585285E-02 1,midg,midg; igrid,midg,midg -0.2342654 9.7029358E-02 gauss-seidel spectral radius is 0.9993113 estimated iterations to convergence 301 setup time was (sec) 2.660000 now iterating at: 19:34:22 rms-change max change #iterations 10.86477 358.6818 at 10iterations 6.621199 146.8905 at 20iterations 3.970065 85.43542 at 30iterations 2.380116 49.43875 at 40iterations 1.418926 28.97004 at 50iterations 0.8425891 15.20556 at 60iterations 0.4992821 8.346531 at 70iterations 0.2953453 5.206717 at 80iterations 0.1739329 2.935583 at 90iterations 0.1026414 1.916541 at 100iterations 6.0426194E-02 1.004360 at 110iterations 3.5544835E-02 0.6703520 at 120iterations 2.0890960E-02 0.3667431 at 130iterations 1.2265649E-02 0.2223530 at 140iterations 7.2078076E-03 0.1239834 at 150iterations 4.2331778E-03 7.1613312E-02 at 160iterations 2.4921175E-03 4.2287827E-02 at 170iterations 1.4744973E-03 2.4454117E-02 at 180iterations finished qdiffx linear iterations at : 19:34:39 total time elapsed so far: 20.48000 # loops : 180 mean,max change (kT/e) : 1.4744973E-03 2.4454117E-02 energy calculations done at 20.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.69000 DelPhi exited at 19:34:40 20.691u 0.501s 0:21.79 97.2% 0+0k 0+0io 0pf+0w