Sun Oct 9 14:48:19 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 Sun Oct 9 2011 at 14:48:19 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2505 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: 0.5631040 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): -20.77300 36.37400 ymin,ymax (A): -22.07500 29.72800 zmin,zma (A): -10.16600 53.05500 x,y,z range (A): 57.14700 51.80300 63.22100 scale (grids/A): 0.5631040 object centre (A): 7.800500 3.826501 21.44450 number of atom coordinates read : 2505 total number of charged atoms : 2364 net assigned charge : 6.000016 assigned positive charge : 377.1167 centred at (gu) : 90.75151 88.96289 86.83669 assigned negative charge : -371.1175 centred at (gu) : 90.49679 89.14211 86.92336 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5381 nv = 96 ne = 84 npr = 46549 no. pairs analyzed = 46549 no. exposed pairs = 3618 no. arc points = 26891 no. surface atoms = 1215 nbur = 1290 mkacc time = 9.9999994E-02 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 = 1.512000 m= 214 mr = 2319 m= 0 mr = 3 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2723 ## 340 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6825 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2683811E-09 -1.0712705E-10 midg,1,midg; midg,igrid,midg 3.1166500E-09 -9.4802521E-10 1,midg,midg; igrid,midg,midg -1.6930669E-09 3.7840509E-09 gauss-seidel spectral radius is 0.9837124 estimated iterations to convergence 64 setup time was (sec) 0.4800000 now iterating at: 14:48:20 rms-change max change #iterations 7.5136758E-02 14.26404 at 10iterations 5.4031485E-03 0.8847694 at 20iterations 4.8048023E-04 0.1146202 at 30iterations 6.9444875E-05 1.8180847E-02 at 40iterations 1.4124622E-05 3.6926270E-03 at 50iterations finished qdiffx linear iterations at : 14:48:22 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.4124622E-05 3.6926270E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 14:48:23 3.101u 0.140s 0:03.52 92.0% 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 Sun Oct 9 2011 at 14:48:23 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2505 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: 1.689312 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): -20.77300 36.37400 ymin,ymax (A): -22.07500 29.72800 zmin,zma (A): -10.16600 53.05500 x,y,z range (A): 57.14700 51.80300 63.22100 scale (grids/A): 1.689312 object centre (A): 7.800500 3.826501 21.44450 number of atom coordinates read : 2505 total number of charged atoms : 2364 net assigned charge : 6.000016 assigned positive charge : 377.1167 centred at (gu) : 92.25373 86.88811 80.50935 assigned negative charge : -371.1175 centred at (gu) : 91.49000 87.42592 80.76990 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 58385 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26891 grid for indexing accessible points = 1.400000 m= 16795 mr = 35401 m= 1764 mr = 10731 m= 79 mr = 789 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 30100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 241 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 18224 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) : 0.5631040 object centre at (A) : 7.800500 3.826501 21.44450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8949050E-02 2.0548317E-04 midg,1,midg; midg,igrid,midg 2.0328717E-02 -8.3278660E-03 1,midg,midg; igrid,midg,midg -2.8767662E-02 2.2869345E-02 gauss-seidel spectral radius is 0.9982772 estimated iterations to convergence 191 setup time was (sec) 0.7000000 now iterating at: 14:48:23 rms-change max change #iterations 3.226274 173.2203 at 10iterations 1.363231 56.43978 at 20iterations 0.5765459 23.47331 at 30iterations 0.2441335 10.54289 at 40iterations 0.1035955 4.069880 at 50iterations 4.3912552E-02 1.678872 at 60iterations 1.8671751E-02 0.7049637 at 70iterations 7.9256073E-03 0.2885199 at 80iterations 3.3926216E-03 0.1187487 at 90iterations 1.4555134E-03 5.5348396E-02 at 100iterations 6.2630390E-04 2.5993347E-02 at 110iterations 2.7208470E-04 1.0986328E-02 at 120iterations finished qdiffx linear iterations at : 14:48:29 total time elapsed so far: 6.610000 # loops : 120 mean,max change (kT/e) : 2.7208470E-04 1.0986328E-02 energy calculations done at 6.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.770000 DelPhi exited at 14:48:30 6.775u 0.193s 0:07.24 96.1% 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 14:48:30 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2505 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: 2.533968 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): -20.77300 36.37400 ymin,ymax (A): -22.07500 29.72800 zmin,zma (A): -10.16600 53.05500 x,y,z range (A): 57.14700 51.80300 63.22100 scale (grids/A): 2.533968 object centre (A): 7.800500 3.826501 21.44450 number of atom coordinates read : 2505 total number of charged atoms : 2364 net assigned charge : 6.000016 assigned positive charge : 377.1167 centred at (gu) : 93.38052 85.33198 75.76397 assigned negative charge : -371.1175 centred at (gu) : 92.23497 86.13881 76.15481 start vw surface at 0.1500000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 135067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26891 grid for indexing accessible points = 1.400000 m= 57584 mr = 87448 m= 16201 mr = 43261 m= 2607 mr = 11484 m= 254 mr = 1592 m= 8 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9700000 number of dielectric boundary points 67807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 18904 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) : 1.689312 object centre at (A) : 7.800500 3.826501 21.44450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5447481 -1.0509448E-02 midg,1,midg; midg,igrid,midg 0.2616046 -0.1165432 1,midg,midg; igrid,midg,midg -0.4263822 0.3676549 gauss-seidel spectral radius is 0.9991602 estimated iterations to convergence 273 setup time was (sec) 1.250000 now iterating at: 14:48:31 rms-change max change #iterations 8.308659 409.9777 at 10iterations 4.722472 115.3826 at 20iterations 2.666760 61.27014 at 30iterations 1.492422 38.61060 at 40iterations 0.8378036 18.05210 at 50iterations 0.4666262 11.51935 at 60iterations 0.2594089 6.197707 at 70iterations 0.1444628 3.197633 at 80iterations 8.0099456E-02 1.733786 at 90iterations 4.4557780E-02 0.9317093 at 100iterations 2.4749108E-02 0.5170135 at 110iterations 1.3709809E-02 0.2942696 at 120iterations 7.5803632E-03 0.1687927 at 130iterations 4.2205043E-03 0.1061468 at 140iterations 2.3424830E-03 5.3308487E-02 at 150iterations 1.3026999E-03 2.6799202E-02 at 160iterations 7.2519487E-04 1.5457153E-02 at 170iterations 4.0689710E-04 9.2506409E-03 at 180iterations finished qdiffx linear iterations at : 14:48:41 total time elapsed so far: 11.36000 # loops : 180 mean,max change (kT/e) : 4.0689710E-04 9.2506409E-03 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.54000 DelPhi exited at 14:48:42 11.543u 0.157s 0:11.99 97.4% 0+0k 0+0io 0pf+0w