Tue Oct 11 03:16:16 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 Tue Oct 11 2011 at 03:16:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2847 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5923954 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): -22.52900 31.89300 ymin,ymax (A): -39.48700 20.60800 zmin,zma (A): -31.68000 26.70000 x,y,z range (A): 54.42200 60.09500 58.38000 scale (grids/A): 0.5923954 object centre (A): 4.682000 -9.439500 -2.490001 number of atom coordinates read : 2847 total number of charged atoms : 2695 net assigned charge : -4.499990 assigned positive charge : 418.3705 centred at (gu) : 88.86478 91.56041 92.01901 assigned negative charge : -422.8715 centred at (gu) : 88.79333 91.51835 91.94864 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6830 nv = 96 ne = 84 npr = 55013 no. pairs analyzed = 55013 no. exposed pairs = 4131 no. arc points = 29125 no. surface atoms = 1373 nbur = 1474 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 = 1.456000 m= 329 mr = 3357 m= 2 mr = 17 m= 0 mr = 0 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 3787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2893 ## 309 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8491 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3621125E-09 1.0849085E-09 midg,1,midg; midg,igrid,midg -1.9979645E-09 -2.9286060E-10 1,midg,midg; igrid,midg,midg -4.8936872E-09 4.9971760E-10 gauss-seidel spectral radius is 0.9852910 estimated iterations to convergence 68 setup time was (sec) 0.6400000 now iterating at: 03:16:17 rms-change max change #iterations 0.1034930 16.49275 at 10iterations 8.5278898E-03 1.412393 at 20iterations 7.7636301E-04 0.1135979 at 30iterations 1.0056319E-04 2.1438599E-02 at 40iterations 2.0557123E-05 4.9190521E-03 at 50iterations finished qdiffx linear iterations at : 03:16:20 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 2.0557123E-05 4.9190521E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 03:16:20 4.157u 0.275s 0:04.76 92.8% 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 Tue Oct 11 2011 at 03:16:20 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 = 2847 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.777186 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): -22.52900 31.89300 ymin,ymax (A): -39.48700 20.60800 zmin,zma (A): -31.68000 26.70000 x,y,z range (A): 54.42200 60.09500 58.38000 scale (grids/A): 1.777186 object centre (A): 4.682000 -9.439500 -2.490001 number of atom coordinates read : 2847 total number of charged atoms : 2695 net assigned charge : -4.499990 assigned positive charge : 418.3705 centred at (gu) : 86.59396 94.68049 96.05605 assigned negative charge : -422.8715 centred at (gu) : 86.37972 94.55483 95.84597 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 73907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29125 grid for indexing accessible points = 1.400000 m= 23993 mr = 47949 m= 2880 mr = 16371 m= 128 mr = 1426 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 376 time to turn everything in is 0.6600000 number of dielectric boundary points 35146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 225 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 21064 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) : 0.5923954 object centre at (A) : 4.682000 -9.439500 -2.490001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3560624E-02 -6.6902270E-03 midg,1,midg; midg,igrid,midg -2.2619028E-02 -1.9290902E-02 1,midg,midg; igrid,midg,midg -3.7230984E-03 2.5726901E-03 gauss-seidel spectral radius is 0.9984754 estimated iterations to convergence 203 setup time was (sec) 0.9700000 now iterating at: 03:16:22 rms-change max change #iterations 3.850362 164.0250 at 10iterations 1.720536 58.90776 at 20iterations 0.7688541 25.29936 at 30iterations 0.3449534 11.89251 at 40iterations 0.1536623 4.779289 at 50iterations 6.8850406E-02 2.245276 at 60iterations 3.0800108E-02 1.012556 at 70iterations 1.3860610E-02 0.4645042 at 80iterations 6.2242369E-03 0.1976604 at 90iterations 2.7883337E-03 9.4407320E-02 at 100iterations 1.2533977E-03 4.2969465E-02 at 110iterations 5.6936342E-04 2.1186829E-02 at 120iterations finished qdiffx linear iterations at : 03:16:30 total time elapsed so far: 9.450000 # loops : 120 mean,max change (kT/e) : 5.6936342E-04 2.1186829E-02 energy calculations done at 9.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.630000 DelPhi exited at 03:16:31 9.637u 0.323s 0:10.27 96.8% 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 Tue Oct 11 2011 at 03:16:31 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 = 2847 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.665779 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): -22.52900 31.89300 ymin,ymax (A): -39.48700 20.60800 zmin,zma (A): -31.68000 26.70000 x,y,z range (A): 54.42200 60.09500 58.38000 scale (grids/A): 2.665779 object centre (A): 4.682000 -9.439500 -2.490001 number of atom coordinates read : 2847 total number of charged atoms : 2695 net assigned charge : -4.499990 assigned positive charge : 418.3705 centred at (gu) : 84.89069 97.02071 99.08385 assigned negative charge : -422.8715 centred at (gu) : 84.56955 96.83217 98.76883 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 171078 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29125 grid for indexing accessible points = 1.400000 m= 79752 mr = 117487 m= 25246 mr = 62254 m= 4681 mr = 18929 m= 510 mr = 3087 m= 21 mr = 254 m= 0 mr = 3 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 1127 time to turn everything in is 1.670000 number of dielectric boundary points 79274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 21554 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) : 1.777186 object centre at (A) : 4.682000 -9.439500 -2.490001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6641778 -0.1069968 midg,1,midg; midg,igrid,midg -0.2948977 -0.1574798 1,midg,midg; igrid,midg,midg -4.6401352E-02 1.7279866E-03 gauss-seidel spectral radius is 0.9992401 estimated iterations to convergence 286 setup time was (sec) 2.000000 now iterating at: 03:16:33 rms-change max change #iterations 9.715986 277.3817 at 10iterations 5.748629 177.0224 at 20iterations 3.353481 84.22437 at 30iterations 1.941734 50.42163 at 40iterations 1.122960 23.91432 at 50iterations 0.6462041 12.71211 at 60iterations 0.3706363 8.000216 at 70iterations 0.2131096 3.897507 at 80iterations 0.1218973 2.431019 at 90iterations 6.9709547E-02 1.214329 at 100iterations 3.9811041E-02 0.7479019 at 110iterations 2.2737728E-02 0.4238071 at 120iterations 1.2984579E-02 0.2406979 at 130iterations 7.4239937E-03 0.1512241 at 140iterations 4.2569446E-03 8.5616112E-02 at 150iterations 2.4411064E-03 4.8107147E-02 at 160iterations 1.4064332E-03 2.7693748E-02 at 170iterations 8.1545807E-04 1.6796112E-02 at 180iterations finished qdiffx linear iterations at : 03:16:47 total time elapsed so far: 16.12000 # loops : 180 mean,max change (kT/e) : 8.1545807E-04 1.6796112E-02 energy calculations done at 16.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.31000 DelPhi exited at 03:16:48 16.316u 0.298s 0:17.07 97.2% 0+0k 0+0io 0pf+0w