Sun Oct 9 09:19:42 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 Sun Oct 9 2011 at 09:19:42 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 = 2780 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: 0.5622325 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): -80.15701 -32.33200 ymin,ymax (A): -36.05900 27.26000 zmin,zma (A): -52.66500 1.113000 x,y,z range (A): 47.82500 63.31900 53.77800 scale (grids/A): 0.5622325 object centre (A): -56.24450 -4.399499 -25.77600 number of atom coordinates read : 2780 total number of charged atoms : 2634 net assigned charge : 2.500013 assigned positive charge : 409.5007 centred at (gu) : 89.56136 88.54369 89.51096 assigned negative charge : -407.0014 centred at (gu) : 89.50986 88.58364 89.57538 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5860 nv = 96 ne = 84 npr = 55327 no. pairs analyzed = 55327 no. exposed pairs = 3681 no. arc points = 25841 no. surface atoms = 1234 nbur = 1546 mkacc time = 0.1600000 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 = 1.540000 m= 263 mr = 2960 m= 0 mr = 18 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2644 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7457 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1037553E-09 -3.8080181E-10 midg,1,midg; midg,igrid,midg 1.0190856E-09 -1.0841122E-10 1,midg,midg; igrid,midg,midg -3.2180086E-10 7.5665674E-10 gauss-seidel spectral radius is 0.9836708 estimated iterations to convergence 64 setup time was (sec) 0.6400000 now iterating at: 09:19:42 rms-change max change #iterations 8.0632716E-02 13.71365 at 10iterations 5.7712384E-03 0.9560804 at 20iterations 4.4272354E-04 9.6282959E-02 at 30iterations 5.7143818E-05 1.1497498E-02 at 40iterations 1.4019330E-05 3.2072067E-03 at 50iterations finished qdiffx linear iterations at : 09:19:46 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 1.4019330E-05 3.2072067E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 09:19:46 4.084u 0.274s 0:04.66 93.3% 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 Sun Oct 9 2011 at 09:19:46 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 = 2780 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: 1.686697 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): -80.15701 -32.33200 ymin,ymax (A): -36.05900 27.26000 zmin,zma (A): -52.66500 1.113000 x,y,z range (A): 47.82500 63.31900 53.77800 scale (grids/A): 1.686697 object centre (A): -56.24450 -4.399499 -25.77600 number of atom coordinates read : 2780 total number of charged atoms : 2634 net assigned charge : 2.500013 assigned positive charge : 409.5007 centred at (gu) : 88.68354 85.63078 88.53242 assigned negative charge : -407.0014 centred at (gu) : 88.52941 85.75069 88.72604 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 64489 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25841 grid for indexing accessible points = 1.400000 m= 21059 mr = 42867 m= 2513 mr = 14690 m= 87 mr = 1316 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 83 time to turn everything in is 0.5900000 number of dielectric boundary points 29268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20315 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) : 0.5622325 object centre at (A) : -56.24450 -4.399499 -25.77600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1006089E-04 -1.0820606E-02 midg,1,midg; midg,igrid,midg -5.8323639E-03 4.5387093E-03 1,midg,midg; igrid,midg,midg 4.7678649E-03 7.4968659E-03 gauss-seidel spectral radius is 0.9982906 estimated iterations to convergence 192 setup time was (sec) 0.8900000 now iterating at: 09:19:47 rms-change max change #iterations 3.360792 170.4878 at 10iterations 1.432182 53.43431 at 20iterations 0.6102223 21.62121 at 30iterations 0.2603878 8.811311 at 40iterations 0.1114494 4.437023 at 50iterations 4.7656104E-02 1.621033 at 60iterations 2.0428825E-02 0.6998615 at 70iterations 8.7381424E-03 0.2939320 at 80iterations 3.7367158E-03 0.1446285 at 90iterations 1.6039909E-03 6.5956116E-02 at 100iterations 6.9247006E-04 2.6943207E-02 at 110iterations 3.0107680E-04 1.0233164E-02 at 120iterations finished qdiffx linear iterations at : 09:19:56 total time elapsed so far: 9.130000 # loops : 120 mean,max change (kT/e) : 3.0107680E-04 1.0233164E-02 energy calculations done at 9.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.310000 DelPhi exited at 09:19:56 9.310u 0.286s 0:09.87 97.1% 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 Sun Oct 9 2011 at 09:19:56 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 = 2780 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: 2.530046 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): -80.15701 -32.33200 ymin,ymax (A): -36.05900 27.26000 zmin,zma (A): -52.66500 1.113000 x,y,z range (A): 47.82500 63.31900 53.77800 scale (grids/A): 2.530046 object centre (A): -56.24450 -4.399499 -25.77600 number of atom coordinates read : 2780 total number of charged atoms : 2634 net assigned charge : 2.500013 assigned positive charge : 409.5007 centred at (gu) : 88.02518 83.44610 87.79852 assigned negative charge : -407.0014 centred at (gu) : 87.79405 83.62602 88.08893 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 148827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25841 grid for indexing accessible points = 1.400000 m= 70932 mr = 104578 m= 22361 mr = 56224 m= 4038 mr = 17018 m= 383 mr = 2723 m= 9 mr = 197 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 352 time to turn everything in is 1.440000 number of dielectric boundary points 65810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 21060 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) : 1.686697 object centre at (A) : -56.24450 -4.399499 -25.77600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7475859E-03 -0.1556355 midg,1,midg; midg,igrid,midg -4.0989436E-02 2.6353851E-02 1,midg,midg; igrid,midg,midg 8.9882217E-02 0.1295592 gauss-seidel spectral radius is 0.9991708 estimated iterations to convergence 274 setup time was (sec) 1.760000 now iterating at: 09:19:58 rms-change max change #iterations 8.567951 277.7029 at 10iterations 4.858234 120.1157 at 20iterations 2.736084 60.88151 at 30iterations 1.541731 37.85379 at 40iterations 0.8637160 17.56408 at 50iterations 0.4833986 10.84563 at 60iterations 0.2699222 6.063477 at 70iterations 0.1501535 3.543778 at 80iterations 8.3864547E-02 1.977696 at 90iterations 4.6780083E-02 1.038597 at 100iterations 2.6027273E-02 0.5580170 at 110iterations 1.4462079E-02 0.3002243 at 120iterations 8.0373678E-03 0.1702079 at 130iterations 4.4793324E-03 8.8627815E-02 at 140iterations 2.4909854E-03 5.4058790E-02 at 150iterations 1.3906442E-03 2.7741432E-02 at 160iterations 7.7726145E-04 1.5971184E-02 at 170iterations 4.3384914E-04 9.4070435E-03 at 180iterations finished qdiffx linear iterations at : 09:20:12 total time elapsed so far: 15.22000 # loops : 180 mean,max change (kT/e) : 4.3384914E-04 9.4070435E-03 energy calculations done at 15.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.40000 DelPhi exited at 09:20:12 15.397u 0.304s 0:16.00 98.0% 0+0k 0+0io 0pf+0w