Mon Oct 10 14:04:18 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 Mon Oct 10 2011 at 14:04:18 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2511 !!! WARNING: LYS 208 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5508107 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): -22.04900 25.13700 ymin,ymax (A): -23.17900 33.13000 zmin,zma (A): -40.09700 24.53500 x,y,z range (A): 47.18600 56.30900 64.63200 scale (grids/A): 0.5508107 object centre (A): 1.544000 4.975501 -7.781000 number of atom coordinates read : 2511 total number of charged atoms : 2372 net assigned charge : -2.271990 assigned positive charge : 380.2413 centred at (gu) : 89.85484 88.83736 92.20706 assigned negative charge : -382.5137 centred at (gu) : 89.85303 88.79469 92.36719 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4997 nv = 96 ne = 84 npr = 49290 no. pairs analyzed = 49290 no. exposed pairs = 3375 no. arc points = 24170 no. surface atoms = 1142 nbur = 1369 mkacc time = 9.0000004E-02 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 = 1.540000 m= 174 mr = 2347 m= 0 mr = 7 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.1900000 number of dielectric boundary points 2817 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2493 ## 348 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6458 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3555360E-10 -2.1707709E-09 midg,1,midg; midg,igrid,midg -5.7090599E-10 1.1081848E-10 1,midg,midg; igrid,midg,midg -1.5504832E-10 -1.2122221E-10 gauss-seidel spectral radius is 0.9829741 estimated iterations to convergence 63 setup time was (sec) 0.3800000 now iterating at: 14:04:19 rms-change max change #iterations 7.0100941E-02 16.00746 at 10iterations 4.7400845E-03 0.8820227 at 20iterations 3.2549092E-04 6.2513351E-02 at 30iterations 2.2247241E-05 3.9386749E-03 at 40iterations 1.4712112E-06 2.7465820E-04 at 50iterations finished qdiffx linear iterations at : 14:04:21 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.4712112E-06 2.7465820E-04 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 14:04:22 3.376u 0.148s 0:03.93 89.3% 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 Mon Oct 10 2011 at 14:04:22 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2511 !!! WARNING: LYS 208 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.652432 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): -22.04900 25.13700 ymin,ymax (A): -23.17900 33.13000 zmin,zma (A): -40.09700 24.53500 x,y,z range (A): 47.18600 56.30900 64.63200 scale (grids/A): 1.652432 object centre (A): 1.544000 4.975501 -7.781000 number of atom coordinates read : 2511 total number of charged atoms : 2372 net assigned charge : -2.271990 assigned positive charge : 380.2413 centred at (gu) : 89.56430 86.51183 96.62075 assigned negative charge : -382.5137 centred at (gu) : 89.55891 86.38389 97.10128 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 55223 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24170 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15668 mr = 35351 m= 1496 mr = 10354 m= 29 mr = 701 m= 0 mr = 3 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 1952 time to turn everything in is 0.2700000 number of dielectric boundary points 26007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 270 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 18165 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) : 0.5508107 object centre at (A) : 1.544000 4.975501 -7.781000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9203415E-02 -2.5146293E-02 midg,1,midg; midg,igrid,midg -8.3416309E-03 -4.1410588E-03 1,midg,midg; igrid,midg,midg 1.9716232E-03 -1.3603149E-03 gauss-seidel spectral radius is 0.9981819 estimated iterations to convergence 186 setup time was (sec) 0.4700000 now iterating at: 14:04:23 rms-change max change #iterations 3.104660 190.2380 at 10iterations 1.287731 60.29596 at 20iterations 0.5376897 22.78705 at 30iterations 0.2218614 8.522192 at 40iterations 9.2228867E-02 4.372142 at 50iterations 3.8503237E-02 1.507274 at 60iterations 1.5921537E-02 0.6336145 at 70iterations 6.6388310E-03 0.2532701 at 80iterations 2.7610012E-03 0.1034470 at 90iterations 1.1453587E-03 4.4198990E-02 at 100iterations 4.7801237E-04 1.8035412E-02 at 110iterations 1.9940706E-04 8.4342957E-03 at 120iterations finished qdiffx linear iterations at : 14:04:30 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 1.9940706E-04 8.4342957E-03 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 14:04:30 7.561u 0.242s 0:08.15 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 Mon Oct 10 2011 at 14:04:30 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2511 !!! WARNING: LYS 208 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.478648 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): -22.04900 25.13700 ymin,ymax (A): -23.17900 33.13000 zmin,zma (A): -40.09700 24.53500 x,y,z range (A): 47.18600 56.30900 64.63200 scale (grids/A): 2.478648 object centre (A): 1.544000 4.975501 -7.781000 number of atom coordinates read : 2511 total number of charged atoms : 2372 net assigned charge : -2.271990 assigned positive charge : 380.2413 centred at (gu) : 89.34636 84.76748 99.93089 assigned negative charge : -382.5137 centred at (gu) : 89.33818 84.57578 100.6520 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 128151 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24170 grid for indexing accessible points = 1.400000 m= 55020 mr = 87032 m= 14718 mr = 42311 m= 2202 mr = 10780 m= 144 mr = 1408 m= 0 mr = 56 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 6551 time to turn everything in is 0.6500000 number of dielectric boundary points 58648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 18958 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) : 1.652432 object centre at (A) : 1.544000 4.975501 -7.781000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5040877 -0.5847448 midg,1,midg; midg,igrid,midg -8.8053897E-02 -1.7228952E-02 1,midg,midg; igrid,midg,midg 6.4850543E-03 -3.1728704E-02 gauss-seidel spectral radius is 0.9991259 estimated iterations to convergence 267 setup time was (sec) 0.8800000 now iterating at: 14:04:31 rms-change max change #iterations 7.990710 305.1414 at 10iterations 4.455098 114.5374 at 20iterations 2.468240 59.01702 at 30iterations 1.362579 31.43233 at 40iterations 0.7478190 18.73970 at 50iterations 0.4112324 9.046024 at 60iterations 0.2252770 4.895670 at 70iterations 0.1232394 2.620823 at 80iterations 6.7492150E-02 1.841557 at 90iterations 3.6809325E-02 0.8828545 at 100iterations 2.0101102E-02 0.4597435 at 110iterations 1.0996653E-02 0.2536941 at 120iterations 6.0050320E-03 0.1324348 at 130iterations 3.2811256E-03 7.2443008E-02 at 140iterations 1.7896192E-03 3.6918640E-02 at 150iterations 9.7886322E-04 2.1507025E-02 at 160iterations 5.3490954E-04 1.1213303E-02 at 170iterations 2.9264583E-04 6.0329437E-03 at 180iterations finished qdiffx linear iterations at : 14:04:42 total time elapsed so far: 11.89000 # loops : 180 mean,max change (kT/e) : 2.9264583E-04 6.0329437E-03 energy calculations done at 11.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 14:04:43 12.035u 0.221s 0:12.73 96.2% 0+0k 0+0io 0pf+0w