Sat Oct 8 14:40:03 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 14:40:04 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3321 !!! WARNING: NAP 1 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6373646 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): -12.13800 43.71700 ymin,ymax (A): -22.22300 22.29900 zmin,zma (A): -8.286000 47.20600 x,y,z range (A): 55.85500 44.52200 55.49200 scale (grids/A): 0.6373646 object centre (A): 15.78950 3.7999153E-02 19.46000 number of atom coordinates read : 3321 total number of charged atoms : 2884 net assigned charge : -0.9999924 assigned positive charge : 453.0335 centred at (gu) : 88.79848 89.66593 92.12064 assigned negative charge : -454.0343 centred at (gu) : 88.75247 89.56102 92.06061 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8307 nv = 96 ne = 84 npr = 63040 no. pairs analyzed = 63040 no. exposed pairs = 3495 no. arc points = 24190 no. surface atoms = 1197 nbur = 2124 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 463 mr = 4916 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2263 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9966 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7130012E-09 9.8865200E-09 midg,1,midg; midg,igrid,midg -1.5887494E-08 1.0871849E-08 1,midg,midg; igrid,midg,midg -9.3814023E-09 3.3676248E-09 gauss-seidel spectral radius is 0.9872805 estimated iterations to convergence 72 setup time was (sec) 0.4200000 now iterating at: 14:40:04 rms-change max change #iterations 0.1586035 20.32616 at 10iterations 1.5619781E-02 2.199577 at 20iterations 1.6878860E-03 0.3208847 at 30iterations 2.3027250E-04 2.8785229E-02 at 40iterations 4.3095635E-05 6.5670013E-03 at 50iterations finished qdiffx linear iterations at : 14:40:07 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 4.3095635E-05 6.5670013E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 14:40:07 3.364u 0.161s 0:03.87 90.9% 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 Sat Oct 8 2011 at 14:40:07 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3321 !!! WARNING: NAP 1 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.912094 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): -12.13800 43.71700 ymin,ymax (A): -22.22300 22.29900 zmin,zma (A): -8.286000 47.20600 x,y,z range (A): 55.85500 44.52200 55.49200 scale (grids/A): 1.912094 object centre (A): 15.78950 3.7999153E-02 19.46000 number of atom coordinates read : 3321 total number of charged atoms : 2884 net assigned charge : -0.9999924 assigned positive charge : 453.0335 centred at (gu) : 86.39486 88.99711 96.36119 assigned negative charge : -454.0343 centred at (gu) : 86.25713 88.68277 96.18150 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 90385 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24190 grid for indexing accessible points = 1.400000 m= 34035 mr = 65412 m= 5495 mr = 25940 m= 330 mr = 3503 m= 0 mr = 123 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 35267 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 22596 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) : 0.6373646 object centre at (A) : 15.78950 3.7999153E-02 19.46000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4498865E-02 1.7200161E-02 midg,1,midg; midg,igrid,midg -4.2496426E-03 1.8683231E-02 1,midg,midg; igrid,midg,midg -4.6533290E-02 7.7766688E-03 gauss-seidel spectral radius is 0.9986812 estimated iterations to convergence 218 setup time was (sec) 0.6500000 now iterating at: 14:40:08 rms-change max change #iterations 4.681653 183.5789 at 10iterations 2.230499 67.26363 at 20iterations 1.056983 32.20045 at 30iterations 0.5034878 15.01720 at 40iterations 0.2380885 6.317787 at 50iterations 0.1136296 3.982449 at 60iterations 5.4100439E-02 1.609826 at 70iterations 2.5749944E-02 0.7397499 at 80iterations 1.2269483E-02 0.3821936 at 90iterations 5.8527482E-03 0.1609197 at 100iterations 2.8083001E-03 9.1553465E-02 at 110iterations 1.3459029E-03 3.8366318E-02 at 120iterations finished qdiffx linear iterations at : 14:40:15 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.3459029E-03 3.8366318E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 14:40:16 7.754u 0.188s 0:08.30 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 14:40:16 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3321 !!! WARNING: NAP 1 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.868140 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): -12.13800 43.71700 ymin,ymax (A): -22.22300 22.29900 zmin,zma (A): -8.286000 47.20600 x,y,z range (A): 55.85500 44.52200 55.49200 scale (grids/A): 2.868140 object centre (A): 15.78950 3.7999153E-02 19.46000 number of atom coordinates read : 3321 total number of charged atoms : 2884 net assigned charge : -0.9999924 assigned positive charge : 453.0335 centred at (gu) : 84.59213 88.49562 99.54153 assigned negative charge : -454.0343 centred at (gu) : 84.38560 88.02398 99.27226 start vw surface at 0.1100000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 209213 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24190 grid for indexing accessible points = 1.400000 m= 110145 mr = 158084 m= 40938 mr = 92345 m= 10099 mr = 33432 m= 1516 mr = 7677 m= 86 mr = 1010 m= 0 mr = 24 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.150000 number of dielectric boundary points 79425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 23051 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) : 1.912094 object centre at (A) : 15.78950 3.7999153E-02 19.46000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1393002 0.2532692 midg,1,midg; midg,igrid,midg 1.7761162E-03 0.2107044 1,midg,midg; igrid,midg,midg -0.7467506 0.1905882 gauss-seidel spectral radius is 0.9992769 estimated iterations to convergence 293 setup time was (sec) 1.380000 now iterating at: 14:40:17 rms-change max change #iterations 10.89555 336.1654 at 10iterations 6.392411 160.2454 at 20iterations 3.738280 83.71878 at 30iterations 2.181944 44.93700 at 40iterations 1.270977 23.14184 at 50iterations 0.7389125 14.06569 at 60iterations 0.4293797 7.546912 at 70iterations 0.2489967 4.581907 at 80iterations 0.1443171 2.602870 at 90iterations 8.3596721E-02 1.416207 at 100iterations 4.8495851E-02 0.8224640 at 110iterations 2.8031725E-02 0.4190388 at 120iterations 1.6267452E-02 0.2753334 at 130iterations 9.4155753E-03 0.1653185 at 140iterations 5.4595280E-03 8.9849472E-02 at 150iterations 3.1829476E-03 5.5215836E-02 at 160iterations 1.8549523E-03 3.1050026E-02 at 170iterations 1.0885489E-03 1.9346975E-02 at 180iterations finished qdiffx linear iterations at : 14:40:29 total time elapsed so far: 12.80000 # loops : 180 mean,max change (kT/e) : 1.0885489E-03 1.9346975E-02 energy calculations done at 12.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 14:40:29 12.939u 0.196s 0:13.42 97.7% 0+0k 0+0io 0pf+0w