Mon Oct 10 16:04:27 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+sph2.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 = amb2.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 Mon Oct 10 2011 at 16:04:27 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4292 !!! WARNING: GLM 133 has a net charge of -0.0940 !!! WARNING: ASP 607 has a net charge of -2.0000 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: 0.5504700 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): -59.22400 -7.739000 ymin,ymax (A): -34.25600 29.56200 zmin,zma (A): -29.18400 35.48800 x,y,z range (A): 51.48500 63.81800 64.67200 scale (grids/A): 0.5504700 object centre (A): -33.48150 -2.347000 3.152001 number of atom coordinates read : 4292 total number of charged atoms : 4187 net assigned charge : 2.406015 assigned positive charge : 648.7830 centred at (gu) : 90.16953 90.24052 88.64581 assigned negative charge : -646.3803 centred at (gu) : 90.19058 90.27244 88.60410 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8484 nv = 96 ne = 84 npr = 86060 no. pairs analyzed = 86060 no. exposed pairs = 5331 no. arc points = 36591 no. surface atoms = 1796 nbur = 2496 mkacc time = 0.1500000 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 = 1.568000 m= 352 mr = 4627 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3783 ## 503 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 11255 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1348616E-10 4.7335719E-10 midg,1,midg; midg,igrid,midg 5.1739957E-10 -1.9009877E-10 1,midg,midg; igrid,midg,midg 4.0853240E-10 -5.6476997E-11 gauss-seidel spectral radius is 0.9830817 estimated iterations to convergence 63 setup time was (sec) 0.5000000 now iterating at: 16:04:27 rms-change max change #iterations 9.4085425E-02 13.76876 at 10iterations 6.8577477E-03 0.8353462 at 20iterations 9.9358754E-04 0.1800232 at 30iterations 3.5433899E-04 5.5469513E-02 at 40iterations 1.4585012E-04 1.9260406E-02 at 50iterations finished qdiffx linear iterations at : 16:04:30 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 1.4585012E-04 1.9260406E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 16:04:31 3.569u 0.171s 0:04.02 92.7% 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 Mon Oct 10 2011 at 16:04:31 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4292 !!! WARNING: GLM 133 has a net charge of -0.0940 !!! WARNING: ASP 607 has a net charge of -2.0000 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: 1.651410 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): -59.22400 -7.739000 ymin,ymax (A): -34.25600 29.56200 zmin,zma (A): -29.18400 35.48800 x,y,z range (A): 51.48500 63.81800 64.67200 scale (grids/A): 1.651410 object centre (A): -33.48150 -2.347000 3.152001 number of atom coordinates read : 4292 total number of charged atoms : 4187 net assigned charge : 2.406015 assigned positive charge : 648.7830 centred at (gu) : 90.50710 90.72054 85.93591 assigned negative charge : -646.3803 centred at (gu) : 90.57147 90.81660 85.81189 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 94922 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36591 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30976 mr = 66947 m= 3472 mr = 21544 m= 90 mr = 1829 m= 0 mr = 11 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 321 time to turn everything in is 0.4600000 number of dielectric boundary points 39129 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 398 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 32133 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) : 0.5504700 object centre at (A) : -33.48150 -2.347000 3.152001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2582530E-03 -5.9609078E-03 midg,1,midg; midg,igrid,midg 1.8099694E-02 1.5195736E-02 1,midg,midg; igrid,midg,midg -1.8103651E-03 -8.2641302E-05 gauss-seidel spectral radius is 0.9983656 estimated iterations to convergence 196 setup time was (sec) 0.6900000 now iterating at: 16:04:32 rms-change max change #iterations 4.209204 155.5344 at 10iterations 1.841655 61.60874 at 20iterations 0.8038579 22.92475 at 30iterations 0.3515442 12.65814 at 40iterations 0.1533280 4.985882 at 50iterations 6.7134753E-02 2.104025 at 60iterations 2.9491385E-02 0.9258652 at 70iterations 1.2999649E-02 0.4445233 at 80iterations 5.7641594E-03 0.1812477 at 90iterations 2.6470658E-03 8.2805634E-02 at 100iterations 1.2853993E-03 3.7197113E-02 at 110iterations 7.0127071E-04 2.3353577E-02 at 120iterations finished qdiffx linear iterations at : 16:04:39 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 7.0127071E-04 2.3353577E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 16:04:40 8.137u 0.237s 0:08.66 96.5% 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 Mon Oct 10 2011 at 16:04:40 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4292 !!! WARNING: GLM 133 has a net charge of -0.0940 !!! WARNING: ASP 607 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.477115 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): -59.22400 -7.739000 ymin,ymax (A): -34.25600 29.56200 zmin,zma (A): -29.18400 35.48800 x,y,z range (A): 51.48500 63.81800 64.67200 scale (grids/A): 2.477115 object centre (A): -33.48150 -2.347000 3.152001 number of atom coordinates read : 4292 total number of charged atoms : 4187 net assigned charge : 2.406015 assigned positive charge : 648.7830 centred at (gu) : 90.76022 91.08047 83.90358 assigned negative charge : -646.3803 centred at (gu) : 90.85688 91.22485 83.71769 start vw surface at 0.1100000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 221185 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36591 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 105526 mr = 163928 m= 31489 mr = 84120 m= 5492 mr = 23934 m= 434 mr = 3804 m= 8 mr = 193 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 1013 time to turn everything in is 1.130000 number of dielectric boundary points 88155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 33458 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) : 1.651410 object centre at (A) : -33.48150 -2.347000 3.152001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3236897 -0.1290026 midg,1,midg; midg,igrid,midg 0.2615134 0.3111121 1,midg,midg; igrid,midg,midg -8.7124249E-03 7.7201300E-03 gauss-seidel spectral radius is 0.9992288 estimated iterations to convergence 284 setup time was (sec) 1.370000 now iterating at: 16:04:41 rms-change max change #iterations 10.93004 300.8960 at 10iterations 6.411853 165.3259 at 20iterations 3.749908 82.47715 at 30iterations 2.175097 49.96626 at 40iterations 1.257231 25.11470 at 50iterations 0.7259169 13.85105 at 60iterations 0.4173597 7.121490 at 70iterations 0.2396073 4.230652 at 80iterations 0.1373360 2.476010 at 90iterations 7.8780405E-02 1.412363 at 100iterations 4.4963073E-02 0.8711071 at 110iterations 2.5775820E-02 0.4655795 at 120iterations 1.4811323E-02 0.2832565 at 130iterations 8.5186781E-03 0.1618347 at 140iterations 4.9447878E-03 9.7654343E-02 at 150iterations 2.9174797E-03 4.9503326E-02 at 160iterations 1.7731206E-03 3.1715393E-02 at 170iterations 1.1282392E-03 2.0694733E-02 at 180iterations finished qdiffx linear iterations at : 16:04:53 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 1.1282392E-03 2.0694733E-02 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 16:04:53 13.037u 0.210s 0:13.52 97.9% 0+0k 0+0io 0pf+0w