Wed Feb 15 08:55:38 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:39 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 = 2480 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5682090 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): 21.13000 68.24800 ymin,ymax (A): -21.39500 41.25800 zmin,zma (A): -19.58700 37.99300 x,y,z range (A): 47.11800 62.65300 57.58000 scale (grids/A): 0.5682090 object centre (A): 44.68900 9.931501 9.203000 number of atom coordinates read : 2480 total number of charged atoms : 2342 net assigned charge : 2.000005 assigned positive charge : 369.3132 centred at (gu) : 88.95696 88.51615 89.40845 assigned negative charge : -367.3138 centred at (gu) : 89.04942 88.54990 89.42072 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5147 nv = 96 ne = 84 npr = 50678 no. pairs analyzed = 50678 no. exposed pairs = 3176 no. arc points = 22656 no. surface atoms = 1074 nbur = 1406 mkacc time = 0.1400000 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= 219 mr = 2575 m= 4 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 2778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2401 ## 336 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6747 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7708820E-10 1.0273549E-10 midg,1,midg; midg,igrid,midg 9.6371444E-10 -9.8805387E-11 1,midg,midg; igrid,midg,midg 1.7736714E-09 -6.7458367E-10 gauss-seidel spectral radius is 0.9839788 estimated iterations to convergence 65 setup time was (sec) 0.6100000 now iterating at: 08:55:39 rms-change max change #iterations 7.7117987E-02 12.87514 at 10iterations 5.6690527E-03 0.9396362 at 20iterations 4.2453755E-04 8.1088066E-02 at 30iterations 3.0464569E-05 5.2852631E-03 at 40iterations 2.3284010E-06 4.4822693E-04 at 50iterations finished qdiffx linear iterations at : 08:55:43 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 2.3284010E-06 4.4822693E-04 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 08:55:44 4.259u 0.317s 0:05.32 85.7% 0+0k 0+0io 6pf+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 Wed Feb 15 2012 at 08:55:44 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 = 2480 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: 1.704627 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): 21.13000 68.24800 ymin,ymax (A): -21.39500 41.25800 zmin,zma (A): -19.58700 37.99300 x,y,z range (A): 47.11800 62.65300 57.58000 scale (grids/A): 1.704627 object centre (A): 44.68900 9.931501 9.203000 number of atom coordinates read : 2480 total number of charged atoms : 2342 net assigned charge : 2.000005 assigned positive charge : 369.3132 centred at (gu) : 86.87038 85.54803 88.22484 assigned negative charge : -367.3138 centred at (gu) : 87.14808 85.64953 88.26198 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 56259 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22656 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17063 mr = 36908 m= 1973 mr = 11688 m= 71 mr = 1072 m= 0 mr = 4 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 680 time to turn everything in is 0.5300000 number of dielectric boundary points 25694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 300 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18133 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) : 0.5682090 object centre at (A) : 44.68900 9.931501 9.203000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0903478E-02 4.5924112E-03 midg,1,midg; midg,igrid,midg 2.0446854E-02 1.3971548E-02 1,midg,midg; igrid,midg,midg 5.3142905E-03 -9.2946989E-03 gauss-seidel spectral radius is 0.9982770 estimated iterations to convergence 191 setup time was (sec) 0.8500000 now iterating at: 08:55:45 rms-change max change #iterations 3.218319 177.3086 at 10iterations 1.366713 60.35083 at 20iterations 0.5831544 23.70365 at 30iterations 0.2477827 9.383459 at 40iterations 0.1050027 3.513420 at 50iterations 4.4774480E-02 1.674430 at 60iterations 1.9093573E-02 0.7406938 at 70iterations 8.1190141E-03 0.3191404 at 80iterations 3.4540077E-03 0.1377773 at 90iterations 1.4716041E-03 5.3736925E-02 at 100iterations 6.2651088E-04 2.4255753E-02 at 110iterations 2.6746947E-04 9.6840858E-03 at 120iterations finished qdiffx linear iterations at : 08:55:54 total time elapsed so far: 9.560000 # loops : 120 mean,max change (kT/e) : 2.6746947E-04 9.6840858E-03 energy calculations done at 9.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.740000 DelPhi exited at 08:55:55 9.747u 0.345s 0:10.57 95.3% 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 Wed Feb 15 2012 at 08:55:55 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 = 2480 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: 2.556941 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): 21.13000 68.24800 ymin,ymax (A): -21.39500 41.25800 zmin,zma (A): -19.58700 37.99300 x,y,z range (A): 47.11800 62.65300 57.58000 scale (grids/A): 2.556941 object centre (A): 44.68900 9.931501 9.203000 number of atom coordinates read : 2480 total number of charged atoms : 2342 net assigned charge : 2.000005 assigned positive charge : 369.3132 centred at (gu) : 85.30532 83.32198 87.33717 assigned negative charge : -367.3138 centred at (gu) : 85.72207 83.47424 87.39293 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 130550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22656 grid for indexing accessible points = 1.400000 m= 58434 mr = 90525 m= 17461 mr = 45832 m= 3133 mr = 13192 m= 272 mr = 2129 m= 5 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 2346 time to turn everything in is 1.250000 number of dielectric boundary points 58037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 18727 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) : 1.704627 object centre at (A) : 44.68900 9.931501 9.203000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2209524 6.5911464E-02 midg,1,midg; midg,igrid,midg 0.4508113 0.2700471 1,midg,midg; igrid,midg,midg 0.1045509 -0.1395393 gauss-seidel spectral radius is 0.9991553 estimated iterations to convergence 272 setup time was (sec) 1.600000 now iterating at: 08:55:57 rms-change max change #iterations 8.138129 317.5399 at 10iterations 4.540399 122.4142 at 20iterations 2.520493 57.09581 at 30iterations 1.397537 32.52939 at 40iterations 0.7775686 16.69041 at 50iterations 0.4297533 10.14501 at 60iterations 0.2370460 5.366884 at 70iterations 0.1308765 2.804337 at 80iterations 7.2254203E-02 1.665207 at 90iterations 3.9846811E-02 0.8861694 at 100iterations 2.1978173E-02 0.4584479 at 110iterations 1.2124711E-02 0.2603049 at 120iterations 6.6785417E-03 0.1404905 at 130iterations 3.6868125E-03 7.9319000E-02 at 140iterations 2.0361049E-03 4.4921875E-02 at 150iterations 1.1218262E-03 2.3121834E-02 at 160iterations 6.1992940E-04 1.3595581E-02 at 170iterations 3.4230427E-04 7.6732635E-03 at 180iterations finished qdiffx linear iterations at : 08:56:10 total time elapsed so far: 15.48000 # loops : 180 mean,max change (kT/e) : 3.4230427E-04 7.6732635E-03 energy calculations done at 15.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.67000 DelPhi exited at 08:56:12 15.669u 0.360s 0:17.02 94.1% 0+0k 0+0io 0pf+0w