Tue Oct 11 06:03:20 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 06:03:20 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 = 2036 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7374723 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): -18.43900 29.83400 ymin,ymax (A): -11.72700 30.68900 zmin,zma (A): -8.507999 37.97400 x,y,z range (A): 48.27300 42.41600 46.48200 scale (grids/A): 0.7374723 object centre (A): 5.697500 9.481001 14.73300 number of atom coordinates read : 2036 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 90.33780 89.82308 91.01371 assigned negative charge : -307.4362 centred at (gu) : 90.27384 89.73438 90.89784 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7666 nv = 96 ne = 84 npr = 40101 no. pairs analyzed = 40101 no. exposed pairs = 2524 no. arc points = 17134 no. surface atoms = 860 nbur = 1176 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 569 mr = 4458 m= 4 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1543 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8191 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6767082E-12 2.5803976E-07 midg,1,midg; midg,igrid,midg 2.4937108E-08 1.8257474E-07 1,midg,midg; igrid,midg,midg 4.5015955E-08 1.7680041E-07 gauss-seidel spectral radius is 0.9904054 estimated iterations to convergence 83 setup time was (sec) 0.3600000 now iterating at: 06:03:20 rms-change max change #iterations 0.2374590 39.51867 at 10iterations 3.1659842E-02 4.138756 at 20iterations 4.4419896E-03 0.6369019 at 30iterations 6.9478323E-04 9.4787598E-02 at 40iterations 1.5453548E-04 2.0654678E-02 at 50iterations finished qdiffx linear iterations at : 06:03:23 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.5453548E-04 2.0654678E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 06:03:24 3.439u 0.194s 0:04.19 86.3% 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 Tue Oct 11 2011 at 06:03:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2036 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.212417 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): -18.43900 29.83400 ymin,ymax (A): -11.72700 30.68900 zmin,zma (A): -8.507999 37.97400 x,y,z range (A): 48.27300 42.41600 46.48200 scale (grids/A): 2.212417 object centre (A): 5.697500 9.481001 14.73300 number of atom coordinates read : 2036 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 91.01349 89.46906 93.04110 assigned negative charge : -307.4362 centred at (gu) : 90.82186 89.20323 92.69362 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80444 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17134 grid for indexing accessible points = 1.400000 m= 34287 mr = 57593 m= 7347 mr = 26443 m= 742 mr = 5075 m= 24 mr = 403 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 33330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 15396 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) : 0.7374723 object centre at (A) : 5.697500 9.481001 14.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9509093E-02 4.5965958E-02 midg,1,midg; midg,igrid,midg 3.0707683E-02 3.0099280E-02 1,midg,midg; igrid,midg,midg 5.0287694E-02 4.5061246E-02 gauss-seidel spectral radius is 0.9989081 estimated iterations to convergence 239 setup time was (sec) 0.6400000 now iterating at: 06:03:25 rms-change max change #iterations 4.903528 215.9776 at 10iterations 2.481207 96.89926 at 20iterations 1.265030 37.94660 at 30iterations 0.6431143 19.41120 at 40iterations 0.3258605 9.891315 at 50iterations 0.1656340 4.687179 at 60iterations 8.4089413E-02 2.674354 at 70iterations 4.3001506E-02 1.201113 at 80iterations 2.1919843E-02 0.6217346 at 90iterations 1.1187999E-02 0.3303569 at 100iterations 5.7378677E-03 0.1776466 at 110iterations 2.9957274E-03 9.0534210E-02 at 120iterations finished qdiffx linear iterations at : 06:03:33 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.9957274E-03 9.0534210E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 06:03:34 7.961u 0.230s 0:09.88 82.8% 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 06:03:34 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 = 2036 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.318625 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): -18.43900 29.83400 ymin,ymax (A): -11.72700 30.68900 zmin,zma (A): -8.507999 37.97400 x,y,z range (A): 48.27300 42.41600 46.48200 scale (grids/A): 3.318625 object centre (A): 5.697500 9.481001 14.73300 number of atom coordinates read : 2036 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 91.52024 89.20369 94.56177 assigned negative charge : -307.4362 centred at (gu) : 91.23277 88.80493 94.04033 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 185309 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17134 grid for indexing accessible points = 1.400000 m= 104284 mr = 138154 m= 45302 mr = 87675 m= 14089 mr = 37689 m= 3073 mr = 11134 m= 395 mr = 2308 m= 23 mr = 273 m= 0 mr = 9 time to grow re-entrant surface = 0.6800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 75233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 15488 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) : 2.212417 object centre at (A) : 5.697500 9.481001 14.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5385197 0.4383597 midg,1,midg; midg,igrid,midg 0.2569295 0.1428362 1,midg,midg; igrid,midg,midg 0.3202970 0.2760854 gauss-seidel spectral radius is 0.9993171 estimated iterations to convergence 302 setup time was (sec) 1.530000 now iterating at: 06:03:36 rms-change max change #iterations 10.78647 318.4567 at 10iterations 6.440969 138.9454 at 20iterations 3.829157 70.26753 at 30iterations 2.279687 43.90839 at 40iterations 1.353170 24.14642 at 50iterations 0.8017522 15.57825 at 60iterations 0.4749916 8.387365 at 70iterations 0.2806807 5.458344 at 80iterations 0.1657242 2.827139 at 90iterations 9.8124035E-02 1.954770 at 100iterations 5.8039717E-02 0.9950254 at 110iterations 3.4532603E-02 0.5400751 at 120iterations 2.0567112E-02 0.3350940 at 130iterations 1.2393354E-02 0.2165794 at 140iterations 7.6330588E-03 0.1281509 at 150iterations 4.8729852E-03 8.7402344E-02 at 160iterations 3.2518038E-03 5.7548523E-02 at 170iterations 2.3191210E-03 4.0672302E-02 at 180iterations finished qdiffx linear iterations at : 06:03:48 total time elapsed so far: 13.34000 # loops : 180 mean,max change (kT/e) : 2.3191210E-03 4.0672302E-02 energy calculations done at 13.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 06:03:49 13.481u 0.210s 0:14.99 91.3% 0+0k 0+0io 0pf+0w