Sat Oct 8 21:26:59 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 8 2011 at 21:26:59 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 = 2617 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: 0.6433192 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): -28.23200 27.10600 ymin,ymax (A): 16.06600 62.39900 zmin,zma (A): -20.65800 26.92400 x,y,z range (A): 55.33800 46.33300 47.58200 scale (grids/A): 0.6433192 object centre (A): -0.5629997 39.23250 3.133000 number of atom coordinates read : 2617 total number of charged atoms : 2479 net assigned charge : 1.500007 assigned positive charge : 394.6258 centred at (gu) : 90.47418 90.44997 89.06178 assigned negative charge : -393.1263 centred at (gu) : 90.48526 90.42662 89.08028 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7432 nv = 96 ne = 84 npr = 52134 no. pairs analyzed = 52134 no. exposed pairs = 3392 no. arc points = 24246 no. surface atoms = 1125 nbur = 1492 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 438 mr = 4000 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3823 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2312 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8729 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7984750E-09 -1.2417730E-12 midg,1,midg; midg,igrid,midg -5.8490701E-10 5.9134369E-09 1,midg,midg; igrid,midg,midg 3.4364784E-09 1.0195007E-09 gauss-seidel spectral radius is 0.9874858 estimated iterations to convergence 73 setup time was (sec) 0.5000000 now iterating at: 21:26:59 rms-change max change #iterations 0.1494922 22.24638 at 10iterations 1.5094204E-02 2.158001 at 20iterations 1.5114227E-03 0.1972711 at 30iterations 1.5839578E-04 2.2918910E-02 at 40iterations 2.3734681E-05 2.8762817E-03 at 50iterations finished qdiffx linear iterations at : 21:27:02 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 2.3734681E-05 2.8762817E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 21:27:02 3.100u 0.143s 0:03.52 92.0% 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 Sat Oct 8 2011 at 21:27:02 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 = 2617 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: 1.929958 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): -28.23200 27.10600 ymin,ymax (A): 16.06600 62.39900 zmin,zma (A): -20.65800 26.92400 x,y,z range (A): 55.33800 46.33300 47.58200 scale (grids/A): 1.929958 object centre (A): -0.5629997 39.23250 3.133000 number of atom coordinates read : 2617 total number of charged atoms : 2479 net assigned charge : 1.500007 assigned positive charge : 394.6258 centred at (gu) : 91.42165 91.34946 87.18467 assigned negative charge : -393.1263 centred at (gu) : 91.45551 91.27956 87.24028 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24246 grid for indexing accessible points = 1.400000 m= 29211 mr = 54654 m= 4933 mr = 20836 m= 324 mr = 2819 m= 4 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 399 time to turn everything in is 0.5500000 number of dielectric boundary points 35474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19556 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) : 0.6433192 object centre at (A) : -0.5629997 39.23250 3.133000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9723170E-02 -6.4491206E-03 midg,1,midg; midg,igrid,midg -5.1594264E-04 1.2468820E-02 1,midg,midg; igrid,midg,midg 2.0122163E-02 -2.7006641E-02 gauss-seidel spectral radius is 0.9986825 estimated iterations to convergence 218 setup time was (sec) 0.8100000 now iterating at: 21:27:03 rms-change max change #iterations 4.403571 168.5822 at 10iterations 2.089612 77.19167 at 20iterations 0.9969070 29.84585 at 30iterations 0.4713349 16.83402 at 40iterations 0.2245406 7.596340 at 50iterations 0.1064633 3.208806 at 60iterations 5.0576307E-02 1.515661 at 70iterations 2.4069199E-02 0.7384415 at 80iterations 1.1381551E-02 0.3471527 at 90iterations 5.4202545E-03 0.1654644 at 100iterations 2.5762205E-03 7.9193115E-02 at 110iterations 1.2237763E-03 4.1800976E-02 at 120iterations finished qdiffx linear iterations at : 21:27:09 total time elapsed so far: 6.690000 # loops : 120 mean,max change (kT/e) : 1.2237763E-03 4.1800976E-02 energy calculations done at 6.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 21:27:10 6.861u 0.181s 0:07.35 95.7% 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 8 2011 at 21:27:10 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 = 2617 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.894937 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): -28.23200 27.10600 ymin,ymax (A): 16.06600 62.39900 zmin,zma (A): -20.65800 26.92400 x,y,z range (A): 55.33800 46.33300 47.58200 scale (grids/A): 2.894937 object centre (A): -0.5629997 39.23250 3.133000 number of atom coordinates read : 2617 total number of charged atoms : 2479 net assigned charge : 1.500007 assigned positive charge : 394.6258 centred at (gu) : 92.13245 92.02389 85.77686 assigned negative charge : -393.1263 centred at (gu) : 92.18325 91.91923 85.86048 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 183362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24246 grid for indexing accessible points = 1.400000 m= 93569 mr = 132270 m= 34419 mr = 75578 m= 8757 mr = 26627 m= 1386 mr = 6163 m= 78 mr = 799 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 1518 time to turn everything in is 1.370000 number of dielectric boundary points 80117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 19832 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) : 1.929958 object centre at (A) : -0.5629997 39.23250 3.133000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2537476 -3.5467476E-02 midg,1,midg; midg,igrid,midg -5.9897065E-02 0.1757009 1,midg,midg; igrid,midg,midg 0.1806240 -0.4780015 gauss-seidel spectral radius is 0.9992820 estimated iterations to convergence 294 setup time was (sec) 1.640000 now iterating at: 21:27:11 rms-change max change #iterations 10.43511 416.8883 at 10iterations 6.242003 147.3841 at 20iterations 3.703465 77.65587 at 30iterations 2.183576 46.02522 at 40iterations 1.288718 25.62534 at 50iterations 0.7557350 13.71437 at 60iterations 0.4422786 8.834366 at 70iterations 0.2581404 5.184345 at 80iterations 0.1508031 2.768890 at 90iterations 8.7788582E-02 1.766100 at 100iterations 5.1117536E-02 1.006645 at 110iterations 2.9704614E-02 0.5203490 at 120iterations 1.7252481E-02 0.3122864 at 130iterations 1.0026246E-02 0.1673260 at 140iterations 5.8289529E-03 0.1006556 at 150iterations 3.3874968E-03 5.9230804E-02 at 160iterations 1.9668275E-03 3.6750793E-02 at 170iterations 1.1415605E-03 2.0555496E-02 at 180iterations finished qdiffx linear iterations at : 21:27:21 total time elapsed so far: 11.35000 # loops : 180 mean,max change (kT/e) : 1.1415605E-03 2.0555496E-02 energy calculations done at 11.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.52000 DelPhi exited at 21:27:22 11.521u 0.186s 0:11.96 97.8% 0+0k 0+0io 0pf+0w