Sun Oct 9 01:48:05 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 Sun Oct 9 2011 at 01:48:05 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2341 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6434820 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): -1.281000 54.04300 ymin,ymax (A): -15.06700 27.50700 zmin,zma (A): 29.36500 83.62100 x,y,z range (A): 55.32400 42.57400 54.25600 scale (grids/A): 0.6434820 object centre (A): 26.38100 6.220000 56.49300 number of atom coordinates read : 2341 total number of charged atoms : 2206 net assigned charge : 10.01402 assigned positive charge : 343.3244 centred at (gu) : 90.34724 88.70025 88.90820 assigned negative charge : -333.3111 centred at (gu) : 90.27650 88.83565 88.91469 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6590 nv = 96 ne = 84 npr = 47243 no. pairs analyzed = 47243 no. exposed pairs = 3088 no. arc points = 22161 no. surface atoms = 1032 nbur = 1309 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 3395 m= 6 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3100000 number of dielectric boundary points 3550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2139 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7782 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0717964E-08 1.2093023E-08 midg,1,midg; midg,igrid,midg 4.0165748E-08 7.3378686E-10 1,midg,midg; igrid,midg,midg 7.4656654E-09 2.5299242E-08 gauss-seidel spectral radius is 0.9874701 estimated iterations to convergence 73 setup time was (sec) 0.5500000 now iterating at: 01:48:06 rms-change max change #iterations 0.1372768 23.82572 at 10iterations 1.3649374E-02 1.844437 at 20iterations 1.4744302E-03 0.2110691 at 30iterations 2.2005961E-04 3.4922123E-02 at 40iterations 5.5046909E-05 1.0530472E-02 at 50iterations finished qdiffx linear iterations at : 01:48:09 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 5.5046909E-05 1.0530472E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 01:48:09 3.460u 0.202s 0:03.95 92.6% 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 01:48:09 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2341 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.930446 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): -1.281000 54.04300 ymin,ymax (A): -15.06700 27.50700 zmin,zma (A): 29.36500 83.62100 x,y,z range (A): 55.32400 42.57400 54.25600 scale (grids/A): 1.930446 object centre (A): 26.38100 6.220000 56.49300 number of atom coordinates read : 2341 total number of charged atoms : 2206 net assigned charge : 10.01402 assigned positive charge : 343.3244 centred at (gu) : 91.04150 86.10062 86.72424 assigned negative charge : -333.3111 centred at (gu) : 90.82929 86.50713 86.74403 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22161 grid for indexing accessible points = 1.400000 m= 25125 mr = 46368 m= 4240 mr = 17885 m= 297 mr = 2532 m= 3 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 32478 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17398 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) : 0.6434820 object centre at (A) : 26.38100 6.220000 56.49300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3329602E-02 3.7425887E-02 midg,1,midg; midg,igrid,midg 3.2867324E-02 -3.7742676E-03 1,midg,midg; igrid,midg,midg 1.1634903E-02 6.0486048E-02 gauss-seidel spectral radius is 0.9986488 estimated iterations to convergence 216 setup time was (sec) 0.8400000 now iterating at: 01:48:10 rms-change max change #iterations 4.018363 203.6036 at 10iterations 1.882762 74.70914 at 20iterations 0.8840077 30.61811 at 30iterations 0.4144558 15.43688 at 40iterations 0.1946211 6.402451 at 50iterations 9.1208875E-02 2.882921 at 60iterations 4.2866617E-02 1.531595 at 70iterations 2.0128103E-02 0.6656003 at 80iterations 9.4895540E-03 0.3546820 at 90iterations 4.4856300E-03 0.1481037 at 100iterations 2.1229619E-03 6.7987204E-02 at 110iterations 1.0159966E-03 3.6701202E-02 at 120iterations finished qdiffx linear iterations at : 01:48:17 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 1.0159966E-03 3.6701202E-02 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 01:48:18 7.602u 0.262s 0:08.47 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 Sun Oct 9 2011 at 01:48:18 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2341 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.895669 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): -1.281000 54.04300 ymin,ymax (A): -15.06700 27.50700 zmin,zma (A): 29.36500 83.62100 x,y,z range (A): 55.32400 42.57400 54.25600 scale (grids/A): 2.895669 object centre (A): 26.38100 6.220000 56.49300 number of atom coordinates read : 2341 total number of charged atoms : 2206 net assigned charge : 10.01402 assigned positive charge : 343.3244 centred at (gu) : 91.56212 84.15075 85.08632 assigned negative charge : -333.3111 centred at (gu) : 91.24400 84.76074 85.11615 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 160791 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22161 grid for indexing accessible points = 1.400000 m= 79748 mr = 112940 m= 30130 mr = 63520 m= 7763 mr = 23677 m= 1264 mr = 5631 m= 102 mr = 808 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 73186 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 17648 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) : 1.930446 object centre at (A) : 26.38100 6.220000 56.49300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3813060 0.4801326 midg,1,midg; midg,igrid,midg 0.3077860 -3.8230192E-02 1,midg,midg; igrid,midg,midg 3.4786526E-02 0.6186593 gauss-seidel spectral radius is 0.9992670 estimated iterations to convergence 291 setup time was (sec) 1.570000 now iterating at: 01:48:20 rms-change max change #iterations 9.593431 379.5341 at 10iterations 5.659033 141.6877 at 20iterations 3.320726 80.79607 at 30iterations 1.944108 41.50710 at 40iterations 1.132921 23.07730 at 50iterations 0.6592539 14.18345 at 60iterations 0.3820468 8.075653 at 70iterations 0.2218305 4.336891 at 80iterations 0.1284295 2.758997 at 90iterations 7.4349575E-02 1.505337 at 100iterations 4.2856738E-02 0.8185081 at 110iterations 2.4832359E-02 0.5025330 at 120iterations 1.4335193E-02 0.2625046 at 130iterations 8.2963975E-03 0.1570452 at 140iterations 4.8060385E-03 8.9422584E-02 at 150iterations 2.7940497E-03 5.5112362E-02 at 160iterations 1.6321426E-03 3.3870697E-02 at 170iterations 9.6351182E-04 2.0679474E-02 at 180iterations finished qdiffx linear iterations at : 01:48:29 total time elapsed so far: 11.27000 # loops : 180 mean,max change (kT/e) : 9.6351182E-04 2.0679474E-02 energy calculations done at 11.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.45000 DelPhi exited at 01:48:30 11.454u 0.221s 0:11.97 97.4% 0+0k 0+0io 0pf+0w