Sun Oct 9 15:38:23 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 15:38:24 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: 238 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5536 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5019175 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): 156.1080 227.0360 ymin,ymax (A): 93.00100 157.0360 zmin,zma (A): -0.9170000 63.62800 x,y,z range (A): 70.92799 64.03501 64.54501 scale (grids/A): 0.5019175 object centre (A): 191.5720 125.0185 31.35550 number of atom coordinates read : 5536 total number of charged atoms : 5363 net assigned charge : -5.999955 assigned positive charge : 846.7128 centred at (gu) : 89.68042 88.90409 90.52267 assigned negative charge : -852.7201 centred at (gu) : 89.78500 88.93900 90.45885 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8384 nv = 96 ne = 84 npr = 116928 no. pairs analyzed = 116928 no. exposed pairs = 6155 no. arc points = 42079 no. surface atoms = 2067 nbur = 3469 mkacc time = 0.2500000 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 = 1.708000 m= 250 mr = 4638 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.5000000 number of dielectric boundary points 3993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4106 ## 586 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 11485 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7067797E-10 8.6317287E-11 midg,1,midg; midg,igrid,midg 1.9848245E-11 -1.0030340E-10 1,midg,midg; igrid,midg,midg 1.7369742E-10 -2.6130426E-10 gauss-seidel spectral radius is 0.9797375 estimated iterations to convergence 58 setup time was (sec) 0.7200000 now iterating at: 15:38:24 rms-change max change #iterations 6.9350243E-02 9.991920 at 10iterations 4.1674958E-03 0.6013870 at 20iterations 4.2164949E-04 6.5425873E-02 at 30iterations 8.6791420E-05 1.4123917E-02 at 40iterations 2.0527605E-05 3.2329559E-03 at 50iterations finished qdiffx linear iterations at : 15:38:27 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 2.0527605E-05 3.2329559E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 15:38:27 3.351u 0.142s 0:03.83 91.1% 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 15:38:27 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: 238 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5536 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.505752 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): 156.1080 227.0360 ymin,ymax (A): 93.00100 157.0360 zmin,zma (A): -0.9170000 63.62800 x,y,z range (A): 70.92799 64.03501 64.54501 scale (grids/A): 1.505752 object centre (A): 191.5720 125.0185 31.35550 number of atom coordinates read : 5536 total number of charged atoms : 5363 net assigned charge : -5.999955 assigned positive charge : 846.7128 centred at (gu) : 89.03990 86.71054 91.56660 assigned negative charge : -852.7201 centred at (gu) : 89.35493 86.81679 91.37624 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 95793 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42079 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27141 mr = 68312 m= 2122 mr = 18655 m= 30 mr = 934 m= 0 mr = 1 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3760 time to turn everything in is 0.6300000 number of dielectric boundary points 37184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 535 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 40012 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) : 0.5019175 object centre at (A) : 191.5720 125.0185 31.35550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3382091E-03 -3.2908556E-03 midg,1,midg; midg,igrid,midg 4.4635297E-03 -1.1299295E-02 1,midg,midg; igrid,midg,midg -2.0134076E-02 -1.1585094E-02 gauss-seidel spectral radius is 0.9980821 estimated iterations to convergence 181 setup time was (sec) 0.8900000 now iterating at: 15:38:28 rms-change max change #iterations 4.007414 173.1966 at 10iterations 1.635190 53.87117 at 20iterations 0.6666155 23.76831 at 30iterations 0.2724954 9.091557 at 40iterations 0.1111521 3.360230 at 50iterations 4.5487773E-02 1.464396 at 60iterations 1.8580779E-02 0.5910654 at 70iterations 7.6114978E-03 0.2209167 at 80iterations 3.1190366E-03 9.3650818E-02 at 90iterations 1.2880998E-03 3.8735390E-02 at 100iterations 5.3365860E-04 1.5909433E-02 at 110iterations 2.2441485E-04 7.8516006E-03 at 120iterations finished qdiffx linear iterations at : 15:38:34 total time elapsed so far: 6.900000 # loops : 120 mean,max change (kT/e) : 2.2441485E-04 7.8516006E-03 energy calculations done at 6.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 15:38:35 7.077u 0.187s 0:07.58 95.6% 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 15:38:35 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: 238 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5536 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.258629 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): 156.1080 227.0360 ymin,ymax (A): 93.00100 157.0360 zmin,zma (A): -0.9170000 63.62800 x,y,z range (A): 70.92799 64.03501 64.54501 scale (grids/A): 2.258629 object centre (A): 191.5720 125.0185 31.35550 number of atom coordinates read : 5536 total number of charged atoms : 5363 net assigned charge : -5.999955 assigned positive charge : 846.7128 centred at (gu) : 88.55925 85.06533 92.34937 assigned negative charge : -852.7201 centred at (gu) : 89.03237 85.22525 92.06417 start vw surface at 0.2200000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 224158 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42079 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 98749 mr = 167719 m= 24130 mr = 78785 m= 3037 mr = 17907 m= 113 mr = 1856 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 12655 time to turn everything in is 1.500000 number of dielectric boundary points 83879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 42779 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) : 1.505752 object centre at (A) : 191.5720 125.0185 31.35550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2406483 -0.1268749 midg,1,midg; midg,igrid,midg 0.1055117 -0.2751992 1,midg,midg; igrid,midg,midg -0.5187900 0.2512465 gauss-seidel spectral radius is 0.9991580 estimated iterations to convergence 272 setup time was (sec) 1.790000 now iterating at: 15:38:37 rms-change max change #iterations 10.85736 258.6245 at 10iterations 6.126616 138.4958 at 20iterations 3.454037 72.21450 at 30iterations 1.935215 38.04018 at 40iterations 1.083081 23.26254 at 50iterations 0.6037607 10.87358 at 60iterations 0.3368939 6.320667 at 70iterations 0.1873873 3.436050 at 80iterations 0.1040443 2.126091 at 90iterations 5.7784617E-02 1.089520 at 100iterations 3.2075554E-02 0.5566440 at 110iterations 1.7810589E-02 0.3357162 at 120iterations 9.8875109E-03 0.1785583 at 130iterations 5.4805414E-03 0.1033440 at 140iterations 3.0426807E-03 5.3819656E-02 at 150iterations 1.6860974E-03 2.9846191E-02 at 160iterations 9.3685556E-04 1.6532898E-02 at 170iterations 5.1907892E-04 9.4919205E-03 at 180iterations finished qdiffx linear iterations at : 15:38:46 total time elapsed so far: 11.26000 # loops : 180 mean,max change (kT/e) : 5.1907892E-04 9.4919205E-03 energy calculations done at 11.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.43000 DelPhi exited at 15:38:47 11.434u 0.179s 0:11.89 97.5% 0+0k 0+0io 0pf+0w