Tue Oct 11 03:52:09 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 Tue Oct 11 2011 at 03:52:09 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: 348 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 235 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6614764 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): -11.34700 37.11900 ymin,ymax (A): -26.84400 21.63800 zmin,zma (A): -8.224999 45.59400 x,y,z range (A): 48.46600 48.48200 53.81900 scale (grids/A): 0.6614764 object centre (A): 12.88600 -2.603000 18.68450 number of atom coordinates read : 2761 total number of charged atoms : 2606 net assigned charge : 0.7010158 assigned positive charge : 419.1058 centred at (gu) : 90.10271 90.37885 91.24515 assigned negative charge : -418.4053 centred at (gu) : 89.79591 90.23821 91.19855 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8079 nv = 96 ne = 84 npr = 57076 no. pairs analyzed = 57076 no. exposed pairs = 3211 no. arc points = 22532 no. surface atoms = 1087 nbur = 1674 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 474 mr = 4735 m= 5 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2100000 number of dielectric boundary points 3756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2231 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9557 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6904842E-09 1.5490793E-08 midg,1,midg; midg,igrid,midg -2.7631421E-08 3.4996052E-08 1,midg,midg; igrid,midg,midg -6.7025326E-08 6.8846205E-08 gauss-seidel spectral radius is 0.9881632 estimated iterations to convergence 75 setup time was (sec) 0.4000000 now iterating at: 03:52:09 rms-change max change #iterations 0.1786869 22.80947 at 10iterations 1.9188100E-02 2.553890 at 20iterations 2.0778764E-03 0.2639465 at 30iterations 2.2750639E-04 2.9305100E-02 at 40iterations 2.9214285E-05 3.9658546E-03 at 50iterations finished qdiffx linear iterations at : 03:52:12 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.9214285E-05 3.9658546E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 03:52:13 3.379u 0.170s 0:03.81 92.9% 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 Tue Oct 11 2011 at 03:52:13 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: 348 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 235 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.984429 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): -11.34700 37.11900 ymin,ymax (A): -26.84400 21.63800 zmin,zma (A): -8.224999 45.59400 x,y,z range (A): 48.46600 48.48200 53.81900 scale (grids/A): 1.984429 object centre (A): 12.88600 -2.603000 18.68450 number of atom coordinates read : 2761 total number of charged atoms : 2606 net assigned charge : 0.7010158 assigned positive charge : 419.1058 centred at (gu) : 90.30759 91.13611 93.73517 assigned negative charge : -418.4053 centred at (gu) : 89.38751 90.71429 93.59532 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 86505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22532 grid for indexing accessible points = 1.400000 m= 33548 mr = 62157 m= 5453 mr = 25552 m= 330 mr = 3445 m= 1 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 439 time to turn everything in is 0.4300000 number of dielectric boundary points 34592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20539 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) : 0.6614764 object centre at (A) : 12.88600 -2.603000 18.68450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4445970E-02 -4.3838462E-03 midg,1,midg; midg,igrid,midg -2.1727536E-02 2.3647619E-02 1,midg,midg; igrid,midg,midg -2.0947741E-02 8.2757205E-02 gauss-seidel spectral radius is 0.9987497 estimated iterations to convergence 224 setup time was (sec) 0.6400000 now iterating at: 03:52:14 rms-change max change #iterations 4.835361 223.1909 at 10iterations 2.348495 80.50144 at 20iterations 1.138719 34.10876 at 30iterations 0.5523474 15.89845 at 40iterations 0.2686619 7.894730 at 50iterations 0.1300065 3.581776 at 60iterations 6.3067563E-02 1.994709 at 70iterations 3.0577037E-02 0.9268532 at 80iterations 1.4890426E-02 0.3996611 at 90iterations 7.2154473E-03 0.2270975 at 100iterations 3.5103837E-03 0.1001711 at 110iterations 1.7051342E-03 4.9736023E-02 at 120iterations finished qdiffx linear iterations at : 03:52:21 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.7051342E-03 4.9736023E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 03:52:21 7.806u 0.197s 0:08.28 96.4% 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 Tue Oct 11 2011 at 03:52:21 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: 348 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 235 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.976644 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): -11.34700 37.11900 ymin,ymax (A): -26.84400 21.63800 zmin,zma (A): -8.224999 45.59400 x,y,z range (A): 48.46600 48.48200 53.81900 scale (grids/A): 2.976644 object centre (A): 12.88600 -2.603000 18.68450 number of atom coordinates read : 2761 total number of charged atoms : 2606 net assigned charge : 0.7010158 assigned positive charge : 419.1058 centred at (gu) : 90.46126 91.70399 95.60257 assigned negative charge : -418.4053 centred at (gu) : 89.08118 91.07129 95.39296 start vw surface at 0.1000000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 199994 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22532 grid for indexing accessible points = 1.400000 m= 106474 mr = 149645 m= 40623 mr = 89160 m= 9886 mr = 33296 m= 1465 mr = 7419 m= 106 mr = 927 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 1327 time to turn everything in is 1.120000 number of dielectric boundary points 78063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 20832 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) : 1.984429 object centre at (A) : 12.88600 -2.603000 18.68450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2532129 0.2168485 midg,1,midg; midg,igrid,midg -0.2294649 0.3333057 1,midg,midg; igrid,midg,midg -7.8487746E-02 0.7051063 gauss-seidel spectral radius is 0.9992843 estimated iterations to convergence 295 setup time was (sec) 1.360000 now iterating at: 03:52:23 rms-change max change #iterations 11.02691 408.5092 at 10iterations 6.486292 135.9811 at 20iterations 3.803899 69.85703 at 30iterations 2.227720 40.40352 at 40iterations 1.302742 22.83026 at 50iterations 0.7586694 13.17532 at 60iterations 0.4436424 7.262653 at 70iterations 0.2584267 4.279256 at 80iterations 0.1505308 2.746045 at 90iterations 8.7413631E-02 1.580654 at 100iterations 5.0921947E-02 0.8666744 at 110iterations 2.9608514E-02 0.4759102 at 120iterations 1.7246323E-02 0.2851830 at 130iterations 1.0026339E-02 0.1867156 at 140iterations 5.8454219E-03 9.7249985E-02 at 150iterations 3.4163585E-03 5.4931641E-02 at 160iterations 1.9969542E-03 3.7984133E-02 at 170iterations 1.1752788E-03 2.0963669E-02 at 180iterations finished qdiffx linear iterations at : 03:52:34 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 1.1752788E-03 2.0963669E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 03:52:35 12.805u 0.204s 0:13.51 96.2% 0+0k 0+0io 0pf+0w