Sat Oct 8 19:02:48 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 Sat Oct 8 2011 at 19:02:48 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2604 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6262093 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): -32.04400 17.59700 ymin,ymax (A): -23.44400 22.79500 zmin,zma (A): -12.47400 44.37600 x,y,z range (A): 49.64100 46.23900 56.85000 scale (grids/A): 0.6262093 object centre (A): -7.223499 -0.3245001 15.95100 number of atom coordinates read : 2604 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 88.64270 89.25008 89.89828 assigned negative charge : -390.4956 centred at (gu) : 88.54216 89.28745 89.79415 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6717 nv = 96 ne = 84 npr = 54695 no. pairs analyzed = 54695 no. exposed pairs = 3036 no. arc points = 21637 no. surface atoms = 1010 nbur = 1594 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3787 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 163 time to turn everything in is 0.3600000 number of dielectric boundary points 3221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2197 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8233 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0190136E-09 1.2407661E-08 midg,1,midg; midg,igrid,midg 8.7579233E-09 1.2910121E-09 1,midg,midg; igrid,midg,midg -5.0213029E-09 9.2466950E-09 gauss-seidel spectral radius is 0.9867885 estimated iterations to convergence 71 setup time was (sec) 0.6300000 now iterating at: 19:02:49 rms-change max change #iterations 0.1359527 21.32060 at 10iterations 1.2933265E-02 1.890879 at 20iterations 1.2218853E-03 0.1945839 at 30iterations 1.1472648E-04 1.8728256E-02 at 40iterations 1.0860899E-05 1.5373230E-03 at 50iterations finished qdiffx linear iterations at : 19:02:53 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.0860899E-05 1.5373230E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 19:02:53 4.165u 0.273s 0:04.72 93.8% 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 19:02:53 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2604 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.878628 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): -32.04400 17.59700 ymin,ymax (A): -23.44400 22.79500 zmin,zma (A): -12.47400 44.37600 x,y,z range (A): 49.64100 46.23900 56.85000 scale (grids/A): 1.878628 object centre (A): -7.223499 -0.3245001 15.95100 number of atom coordinates read : 2604 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 85.92787 87.74980 89.69420 assigned negative charge : -390.4956 centred at (gu) : 85.62628 87.86207 89.38213 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21637 grid for indexing accessible points = 1.400000 m= 25767 mr = 50941 m= 3823 mr = 19232 m= 190 mr = 2380 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 6208 time to turn everything in is 0.6500000 number of dielectric boundary points 29865 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 19343 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) : 0.6262093 object centre at (A) : -7.223499 -0.3245001 15.95100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9437609E-02 2.4513984E-02 midg,1,midg; midg,igrid,midg 1.5045692E-02 2.8986037E-03 1,midg,midg; igrid,midg,midg -3.7768872E-03 3.1144449E-02 gauss-seidel spectral radius is 0.9985956 estimated iterations to convergence 212 setup time was (sec) 0.9600000 now iterating at: 19:02:54 rms-change max change #iterations 4.168405 230.6883 at 10iterations 1.930576 71.56448 at 20iterations 0.8942802 27.76872 at 30iterations 0.4126373 14.43867 at 40iterations 0.1919003 6.047165 at 50iterations 8.8958815E-02 2.823868 at 60iterations 4.1227415E-02 1.507050 at 70iterations 1.9094363E-02 0.6042023 at 80iterations 8.8478392E-03 0.2920084 at 90iterations 4.0955031E-03 0.1382294 at 100iterations 1.9027997E-03 6.1040878E-02 at 110iterations 8.7960291E-04 2.8476715E-02 at 120iterations finished qdiffx linear iterations at : 19:03:03 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 8.7960291E-04 2.8476715E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 19:03:03 9.616u 0.298s 0:10.20 97.0% 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 19:03:03 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2604 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.817942 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): -32.04400 17.59700 ymin,ymax (A): -23.44400 22.79500 zmin,zma (A): -12.47400 44.37600 x,y,z range (A): 49.64100 46.23900 56.85000 scale (grids/A): 2.817942 object centre (A): -7.223499 -0.3245001 15.95100 number of atom coordinates read : 2604 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 83.89171 86.62453 89.54119 assigned negative charge : -390.4956 centred at (gu) : 83.43953 86.79295 89.07330 start vw surface at 0.1700000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 168040 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21637 grid for indexing accessible points = 1.400000 m= 84810 mr = 123301 m= 29667 mr = 70057 m= 6882 mr = 23874 m= 906 mr = 5150 m= 35 mr = 610 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 21507 time to turn everything in is 1.640000 number of dielectric boundary points 67338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 19728 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) : 1.878628 object centre at (A) : -7.223499 -0.3245001 15.95100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1319728 0.2963600 midg,1,midg; midg,igrid,midg 0.1754130 3.2842293E-02 1,midg,midg; igrid,midg,midg -3.3315025E-02 0.3849024 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 1.970000 now iterating at: 19:03:06 rms-change max change #iterations 9.676592 356.6461 at 10iterations 5.572824 113.6772 at 20iterations 3.184790 64.40013 at 30iterations 1.817317 37.36570 at 40iterations 1.040090 18.51004 at 50iterations 0.5925063 10.43069 at 60iterations 0.3379478 6.255123 at 70iterations 0.1932436 3.627600 at 80iterations 0.1099589 1.998419 at 90iterations 6.2723607E-02 1.208084 at 100iterations 3.5798911E-02 0.7061834 at 110iterations 2.0387011E-02 0.3838673 at 120iterations 1.1622645E-02 0.2563324 at 130iterations 6.6390573E-03 0.1207581 at 140iterations 3.7786576E-03 6.8793297E-02 at 150iterations 2.1570006E-03 3.8653374E-02 at 160iterations 1.2287139E-03 2.2621870E-02 at 170iterations 7.0082117E-04 1.2508392E-02 at 180iterations finished qdiffx linear iterations at : 19:03:20 total time elapsed so far: 15.91000 # loops : 180 mean,max change (kT/e) : 7.0082117E-04 1.2508392E-02 energy calculations done at 15.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.10000 DelPhi exited at 19:03:20 16.097u 0.311s 0:16.72 98.0% 0+0k 0+0io 0pf+0w