Sat Oct 15 14:31:34 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 Sat Oct 15 2011 at 14:31:34 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 = 2870 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5821940 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): -30.37100 30.77700 ymin,ymax (A): 11.01300 57.65500 zmin,zma (A): -1.607000 46.43800 x,y,z range (A): 61.14800 46.64200 48.04500 scale (grids/A): 0.5821940 object centre (A): 0.2030001 34.33400 22.41550 number of atom coordinates read : 2870 total number of charged atoms : 2730 net assigned charge : 0.5000190 assigned positive charge : 430.8432 centred at (gu) : 90.83210 90.09972 90.70588 assigned negative charge : -430.3442 centred at (gu) : 90.81683 90.29709 90.80383 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6361 nv = 96 ne = 84 npr = 57370 no. pairs analyzed = 57370 no. exposed pairs = 3681 no. arc points = 25809 no. surface atoms = 1245 nbur = 1625 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 = 1.484000 m= 279 mr = 3286 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.2100000 number of dielectric boundary points 3335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2639 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8129 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9981079E-09 -2.5169968E-09 midg,1,midg; midg,igrid,midg 4.4513255E-09 -4.5907811E-09 1,midg,midg; igrid,midg,midg -1.6903016E-10 5.9935168E-10 gauss-seidel spectral radius is 0.9847645 estimated iterations to convergence 67 setup time was (sec) 0.4200000 now iterating at: 14:31:34 rms-change max change #iterations 9.6943207E-02 15.45490 at 10iterations 7.5316522E-03 1.165404 at 20iterations 6.0748088E-04 9.6488953E-02 at 30iterations 4.7895715E-05 7.2784424E-03 at 40iterations 3.9804177E-06 5.9080124E-04 at 50iterations finished qdiffx linear iterations at : 14:31:38 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 3.9804177E-06 5.9080124E-04 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 14:31:39 3.731u 0.198s 0:04.74 82.7% 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 Sat Oct 15 2011 at 14:31:39 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 = 2870 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.746582 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): -30.37100 30.77700 ymin,ymax (A): 11.01300 57.65500 zmin,zma (A): -1.607000 46.43800 x,y,z range (A): 61.14800 46.64200 48.04500 scale (grids/A): 1.746582 object centre (A): 0.2030001 34.33400 22.41550 number of atom coordinates read : 2870 total number of charged atoms : 2730 net assigned charge : 0.5000190 assigned positive charge : 430.8432 centred at (gu) : 92.49559 90.29868 92.11674 assigned negative charge : -430.3442 centred at (gu) : 92.45038 90.89091 92.41114 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25809 grid for indexing accessible points = 1.400000 m= 22487 mr = 46811 m= 2705 mr = 15628 m= 102 mr = 1366 m= 0 mr = 25 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1264 time to turn everything in is 0.3600000 number of dielectric boundary points 31060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 221 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 21250 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) : 0.5821940 object centre at (A) : 0.2030001 34.33400 22.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0477868E-03 -6.4571607E-03 midg,1,midg; midg,igrid,midg 1.7260436E-02 -2.6197920E-02 1,midg,midg; igrid,midg,midg 4.9891113E-03 6.3399049E-03 gauss-seidel spectral radius is 0.9984093 estimated iterations to convergence 199 setup time was (sec) 0.6000000 now iterating at: 14:31:40 rms-change max change #iterations 3.738432 178.3730 at 10iterations 1.637416 56.61939 at 20iterations 0.7194219 23.69235 at 30iterations 0.3173135 11.36112 at 40iterations 0.1395094 4.770184 at 50iterations 6.1520383E-02 2.095247 at 60iterations 2.7054958E-02 0.8571053 at 70iterations 1.1936830E-02 0.4161054 at 80iterations 5.2668205E-03 0.1739364 at 90iterations 2.3155904E-03 8.0482483E-02 at 100iterations 1.0229191E-03 3.1673431E-02 at 110iterations 4.4947272E-04 1.5368104E-02 at 120iterations finished qdiffx linear iterations at : 14:31:55 total time elapsed so far: 8.390000 # loops : 120 mean,max change (kT/e) : 4.4947272E-04 1.5368104E-02 energy calculations done at 8.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.510000 DelPhi exited at 14:31:56 8.512u 0.293s 0:17.03 51.6% 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 Sat Oct 15 2011 at 14:31:56 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 = 2870 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.619873 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): -30.37100 30.77700 ymin,ymax (A): 11.01300 57.65500 zmin,zma (A): -1.607000 46.43800 x,y,z range (A): 61.14800 46.64200 48.04500 scale (grids/A): 2.619873 object centre (A): 0.2030001 34.33400 22.41550 number of atom coordinates read : 2870 total number of charged atoms : 2730 net assigned charge : 0.5000190 assigned positive charge : 430.8432 centred at (gu) : 93.74318 90.44764 93.17503 assigned negative charge : -430.3442 centred at (gu) : 93.67538 91.33630 93.61662 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 161124 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25809 grid for indexing accessible points = 1.400000 m= 75816 mr = 114268 m= 23794 mr = 60104 m= 4379 mr = 18177 m= 461 mr = 2823 m= 19 mr = 274 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 4380 time to turn everything in is 0.8900000 number of dielectric boundary points 69947 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 21831 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) : 1.746582 object centre at (A) : 0.2030001 34.33400 22.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7648972E-02 -6.5261304E-02 midg,1,midg; midg,igrid,midg 0.2341224 -0.2986359 1,midg,midg; igrid,midg,midg 5.5646218E-02 0.1265544 gauss-seidel spectral radius is 0.9992073 estimated iterations to convergence 280 setup time was (sec) 1.130000 now iterating at: 14:31:57 rms-change max change #iterations 9.446141 338.8738 at 10iterations 5.446623 131.1883 at 20iterations 3.111395 70.52937 at 30iterations 1.769823 44.52212 at 40iterations 1.004190 19.01359 at 50iterations 0.5692203 11.15691 at 60iterations 0.3218385 6.403611 at 70iterations 0.1820364 3.498485 at 80iterations 0.1024596 1.988129 at 90iterations 5.7844225E-02 1.142954 at 100iterations 3.2528017E-02 0.6073494 at 110iterations 1.8341234E-02 0.3727670 at 120iterations 1.0339070E-02 0.2036343 at 130iterations 5.8076736E-03 0.1177311 at 140iterations 3.2742203E-03 5.9656143E-02 at 150iterations 1.8412828E-03 3.8138390E-02 at 160iterations 1.0346358E-03 2.0458221E-02 at 170iterations 5.8348622E-04 1.2031555E-02 at 180iterations finished qdiffx linear iterations at : 14:32:19 total time elapsed so far: 13.62000 # loops : 180 mean,max change (kT/e) : 5.8348622E-04 1.2031555E-02 energy calculations done at 13.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.75000 DelPhi exited at 14:32:19 13.751u 0.230s 0:23.78 58.7% 0+0k 0+0io 0pf+0w