Sun Oct 9 13:33:41 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 13:33:42 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 = 2356 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7130268 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): -5.927000 43.65000 ymin,ymax (A): -13.98400 35.94400 zmin,zma (A): 1.929000 43.71700 x,y,z range (A): 49.57700 49.92800 41.78800 scale (grids/A): 0.7130268 object centre (A): 18.86150 10.98000 22.82300 number of atom coordinates read : 2356 total number of charged atoms : 2216 net assigned charge : 4.500011 assigned positive charge : 358.3491 centred at (gu) : 89.29465 91.50460 90.99226 assigned negative charge : -353.8496 centred at (gu) : 89.29664 91.64645 91.03830 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8189 nv = 96 ne = 84 npr = 47400 no. pairs analyzed = 47400 no. exposed pairs = 2873 no. arc points = 20274 no. surface atoms = 968 nbur = 1388 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 543 mr = 4636 m= 0 mr = 98 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.1800000 number of dielectric boundary points 3998 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1857 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8990 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1267599E-08 1.8643226E-08 midg,1,midg; midg,igrid,midg 9.9865048E-08 -6.3109312E-08 1,midg,midg; igrid,midg,midg 5.2853352E-08 3.8401605E-08 gauss-seidel spectral radius is 0.9897759 estimated iterations to convergence 80 setup time was (sec) 0.3700000 now iterating at: 13:33:42 rms-change max change #iterations 0.2156890 30.89533 at 10iterations 2.7679900E-02 3.503820 at 20iterations 3.9888415E-03 0.4540052 at 30iterations 8.3770556E-04 0.1242409 at 40iterations 2.6890941E-04 3.9249420E-02 at 50iterations finished qdiffx linear iterations at : 13:33:45 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 2.6890941E-04 3.9249420E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 13:33:45 3.319u 0.168s 0:03.73 93.0% 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 13:33:45 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 = 2356 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.139080 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): -5.927000 43.65000 ymin,ymax (A): -13.98400 35.94400 zmin,zma (A): 1.929000 43.71700 x,y,z range (A): 49.57700 49.92800 41.78800 scale (grids/A): 2.139080 object centre (A): 18.86150 10.98000 22.82300 number of atom coordinates read : 2356 total number of charged atoms : 2216 net assigned charge : 4.500011 assigned positive charge : 358.3491 centred at (gu) : 87.88384 94.51350 92.97654 assigned negative charge : -353.8496 centred at (gu) : 87.88947 94.93923 93.11478 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 86706 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20274 grid for indexing accessible points = 1.400000 m= 34568 mr = 60956 m= 6745 mr = 26275 m= 727 mr = 4421 m= 16 mr = 414 m= 0 mr = 1 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 178 time to turn everything in is 0.4200000 number of dielectric boundary points 36695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17609 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) : 0.7130268 object centre at (A) : 18.86150 10.98000 22.82300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6900097E-02 1.5691403E-02 midg,1,midg; midg,igrid,midg 2.3300434E-02 -4.0006924E-02 1,midg,midg; igrid,midg,midg 6.0066644E-02 -1.8640906E-02 gauss-seidel spectral radius is 0.9988788 estimated iterations to convergence 236 setup time was (sec) 0.6400000 now iterating at: 13:33:46 rms-change max change #iterations 5.059948 189.5297 at 10iterations 2.534482 78.49284 at 20iterations 1.271877 36.08052 at 30iterations 0.6398659 18.53494 at 40iterations 0.3232538 8.950856 at 50iterations 0.1621612 4.835770 at 60iterations 8.1922360E-02 2.231373 at 70iterations 4.1379660E-02 1.197731 at 80iterations 2.0975437E-02 0.5415154 at 90iterations 1.0677652E-02 0.2877426 at 100iterations 5.5391300E-03 0.1501389 at 110iterations 2.9521903E-03 8.1665993E-02 at 120iterations finished qdiffx linear iterations at : 13:33:53 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 2.9521903E-03 8.1665993E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 13:33:54 7.779u 0.194s 0:08.26 96.3% 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 Sun Oct 9 2011 at 13:33:54 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 = 2356 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.208620 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): -5.927000 43.65000 ymin,ymax (A): -13.98400 35.94400 zmin,zma (A): 1.929000 43.71700 x,y,z range (A): 49.57700 49.92800 41.78800 scale (grids/A): 3.208620 object centre (A): 18.86150 10.98000 22.82300 number of atom coordinates read : 2356 total number of charged atoms : 2216 net assigned charge : 4.500011 assigned positive charge : 358.3491 centred at (gu) : 86.82558 96.77012 94.46458 assigned negative charge : -353.8496 centred at (gu) : 86.83418 97.40879 94.67215 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 199531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20274 grid for indexing accessible points = 1.400000 m= 107648 mr = 146604 m= 43828 mr = 89386 m= 12637 mr = 36068 m= 2753 mr = 9753 m= 420 mr = 2052 m= 14 mr = 291 m= 0 mr = 6 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 621 time to turn everything in is 1.330000 number of dielectric boundary points 82671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 17726 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) : 2.139080 object centre at (A) : 18.86150 10.98000 22.82300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4506765 -1.7681256E-03 midg,1,midg; midg,igrid,midg 0.3538529 -0.5444789 1,midg,midg; igrid,midg,midg 0.5957575 -0.5384386 gauss-seidel spectral radius is 0.9993105 estimated iterations to convergence 300 setup time was (sec) 1.560000 now iterating at: 13:33:55 rms-change max change #iterations 11.22252 467.8589 at 10iterations 6.702791 137.5229 at 20iterations 3.988536 79.91443 at 30iterations 2.371514 47.63490 at 40iterations 1.402225 23.84371 at 50iterations 0.8302382 14.04684 at 60iterations 0.4901759 8.538956 at 70iterations 0.2896931 5.982724 at 80iterations 0.1705433 3.371681 at 90iterations 0.1003930 1.631960 at 100iterations 5.9420280E-02 1.072520 at 110iterations 3.5254117E-02 0.6071930 at 120iterations 2.1009715E-02 0.3334637 at 130iterations 1.2745610E-02 0.2447395 at 140iterations 7.9314876E-03 0.1470184 at 150iterations 5.1558269E-03 9.8674774E-02 at 160iterations 3.5521411E-03 7.0396423E-02 at 170iterations 2.6142222E-03 5.1156998E-02 at 180iterations finished qdiffx linear iterations at : 13:34:07 total time elapsed so far: 13.13000 # loops : 180 mean,max change (kT/e) : 2.6142222E-03 5.1156998E-02 energy calculations done at 13.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.27000 DelPhi exited at 13:34:07 13.267u 0.203s 0:13.76 97.8% 0+0k 0+0io 0pf+0w