Mon Oct 10 13:59:22 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 13:59:22 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3382 !!! WARNING: LLP 1 has a net charge of 1.1100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5755488 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): -11.03000 50.82400 ymin,ymax (A): -12.76800 42.35400 zmin,zma (A): 19.54500 75.67800 x,y,z range (A): 61.85400 55.12200 56.13300 scale (grids/A): 0.5755488 object centre (A): 19.89700 14.79300 47.61150 number of atom coordinates read : 3382 total number of charged atoms : 3225 net assigned charge : 4.610016 assigned positive charge : 525.1460 centred at (gu) : 90.81189 89.94363 87.74849 assigned negative charge : -520.5370 centred at (gu) : 90.73080 90.00874 87.74532 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7545 nv = 96 ne = 84 npr = 65437 no. pairs analyzed = 65437 no. exposed pairs = 4531 no. arc points = 32378 no. surface atoms = 1518 nbur = 1864 mkacc time = 0.1900000 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= 403 mr = 3805 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 4112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3113 ## 302 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 9368 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2955623E-09 5.4816307E-10 midg,1,midg; midg,igrid,midg 2.2979338E-09 -5.9762933E-10 1,midg,midg; igrid,midg,midg -7.8836088E-10 3.1697804E-09 gauss-seidel spectral radius is 0.9844606 estimated iterations to convergence 66 setup time was (sec) 0.7000000 now iterating at: 13:59:23 rms-change max change #iterations 9.9698842E-02 16.74069 at 10iterations 7.6632081E-03 1.198221 at 20iterations 6.0630270E-04 9.0951920E-02 at 30iterations 7.7145698E-05 1.2819290E-02 at 40iterations 3.3796103E-05 4.7521591E-03 at 50iterations finished qdiffx linear iterations at : 13:59:27 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 3.3796103E-05 4.7521591E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 13:59:27 4.311u 0.300s 0:05.15 89.5% 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 13:59:27 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3382 !!! WARNING: LLP 1 has a net charge of 1.1100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.726647 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): -11.03000 50.82400 ymin,ymax (A): -12.76800 42.35400 zmin,zma (A): 19.54500 75.67800 x,y,z range (A): 61.85400 55.12200 56.13300 scale (grids/A): 1.726647 object centre (A): 19.89700 14.79300 47.61150 number of atom coordinates read : 3382 total number of charged atoms : 3225 net assigned charge : 4.610016 assigned positive charge : 525.1460 centred at (gu) : 92.43518 89.82994 83.24474 assigned negative charge : -520.5370 centred at (gu) : 92.19229 90.02572 83.23556 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 82289 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32378 grid for indexing accessible points = 1.400000 m= 27607 mr = 55035 m= 3743 mr = 18725 m= 167 mr = 1936 m= 0 mr = 31 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 38079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 24985 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) : 0.5755488 object centre at (A) : 19.89700 14.79300 47.61150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2893755E-02 5.8958032E-03 midg,1,midg; midg,igrid,midg 2.4411777E-02 -5.3240992E-03 1,midg,midg; igrid,midg,midg -8.5675437E-03 -8.3339214E-03 gauss-seidel spectral radius is 0.9984299 estimated iterations to convergence 200 setup time was (sec) 1.050000 now iterating at: 13:59:36 rms-change max change #iterations 4.177335 194.3488 at 10iterations 1.849380 69.96342 at 20iterations 0.8230726 28.42400 at 30iterations 0.3649096 12.65294 at 40iterations 0.1625579 6.076013 at 50iterations 7.2274759E-02 2.410560 at 60iterations 3.2125670E-02 1.003953 at 70iterations 1.4307218E-02 0.4678183 at 80iterations 6.3726678E-03 0.2164688 at 90iterations 2.8613051E-03 9.6922874E-02 at 100iterations 1.2939569E-03 4.3525696E-02 at 110iterations 6.1397365E-04 2.1254301E-02 at 120iterations finished qdiffx linear iterations at : 13:59:45 total time elapsed so far: 9.810000 # loops : 120 mean,max change (kT/e) : 6.1397365E-04 2.1254301E-02 energy calculations done at 9.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.990000 DelPhi exited at 13:59:46 9.996u 0.498s 0:18.52 56.5% 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 13:59:47 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3382 !!! WARNING: LLP 1 has a net charge of 1.1100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.589970 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): -11.03000 50.82400 ymin,ymax (A): -12.76800 42.35400 zmin,zma (A): 19.54500 75.67800 x,y,z range (A): 61.85400 55.12200 56.13300 scale (grids/A): 2.589970 object centre (A): 19.89700 14.79300 47.61150 number of atom coordinates read : 3382 total number of charged atoms : 3225 net assigned charge : 4.610016 assigned positive charge : 525.1460 centred at (gu) : 93.65255 89.74485 79.86680 assigned negative charge : -520.5370 centred at (gu) : 93.28826 90.03855 79.85329 start vw surface at 0.1800000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 190842 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32378 grid for indexing accessible points = 1.400000 m= 91562 mr = 134971 m= 29735 mr = 71469 m= 6135 mr = 22202 m= 658 mr = 4023 m= 28 mr = 374 m= 0 mr = 7 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.880000 number of dielectric boundary points 85914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 25783 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) : 1.726647 object centre at (A) : 19.89700 14.79300 47.61150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2222973 7.4476853E-02 midg,1,midg; midg,igrid,midg 0.3696886 -8.2295433E-02 1,midg,midg; igrid,midg,midg 9.4385132E-02 -0.5715076 gauss-seidel spectral radius is 0.9992278 estimated iterations to convergence 284 setup time was (sec) 2.230000 now iterating at: 13:59:49 rms-change max change #iterations 10.62244 301.9772 at 10iterations 6.299052 170.6348 at 20iterations 3.677193 86.18118 at 30iterations 2.140542 47.25357 at 40iterations 1.235206 26.14716 at 50iterations 0.7105695 15.82361 at 60iterations 0.4089807 9.097107 at 70iterations 0.2337622 5.579205 at 80iterations 0.1339127 2.675374 at 90iterations 7.6610930E-02 1.596989 at 100iterations 4.3728594E-02 0.9732323 at 110iterations 2.4984196E-02 0.5252151 at 120iterations 1.4245834E-02 0.2728920 at 130iterations 8.1285881E-03 0.1513720 at 140iterations 4.6569291E-03 9.9792480E-02 at 150iterations 2.6762560E-03 5.3346634E-02 at 160iterations 1.5691883E-03 3.4606695E-02 at 170iterations 9.4808009E-04 1.9819260E-02 at 180iterations finished qdiffx linear iterations at : 14:00:04 total time elapsed so far: 16.97000 # loops : 180 mean,max change (kT/e) : 9.4808009E-04 1.9819260E-02 energy calculations done at 16.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.16000 DelPhi exited at 14:00:06 17.158u 0.334s 0:19.08 91.6% 0+0k 0+0io 0pf+0w