Sun Oct 9 20:44:13 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 20:44:13 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5082 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: SEP 674 has a net charge of -0.4750 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5695453 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): 1.872000 64.37800 ymin,ymax (A): -7.714000 54.61100 zmin,zma (A): -1.135000 59.96300 x,y,z range (A): 62.50600 62.32500 61.09800 scale (grids/A): 0.5695453 object centre (A): 33.12500 23.44850 29.41400 number of atom coordinates read : 5082 total number of charged atoms : 4926 net assigned charge : 2.660028 assigned positive charge : 783.5439 centred at (gu) : 88.37827 88.90887 89.48093 assigned negative charge : -780.8895 centred at (gu) : 88.27357 88.88309 89.44105 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 10654 nv = 96 ne = 84 npr = 103799 no. pairs analyzed = 103799 no. exposed pairs = 5966 no. arc points = 39513 no. surface atoms = 2045 nbur = 3037 mkacc time = 0.2700000 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 = 1.512000 m= 542 mr = 6104 m= 0 mr = 43 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 5049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4112 ## 448 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 13976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0183864E-10 1.3607335E-09 midg,1,midg; midg,igrid,midg -3.0969904E-10 8.9756880E-10 1,midg,midg; igrid,midg,midg -3.5816161E-09 2.2158582E-09 gauss-seidel spectral radius is 0.9842476 estimated iterations to convergence 65 setup time was (sec) 0.8400000 now iterating at: 20:44:14 rms-change max change #iterations 0.1264990 19.53598 at 10iterations 1.2400067E-02 1.860977 at 20iterations 3.6175395E-03 0.4041748 at 30iterations 1.7393293E-03 0.1779671 at 40iterations 8.7398547E-04 9.3851566E-02 at 50iterations finished qdiffx linear iterations at : 20:44:18 total time elapsed so far: 4.600000 # loops : 50 mean,max change (kT/e) : 8.7398547E-04 9.3851566E-02 energy calculations done at 4.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 20:44:18 4.772u 0.385s 0:05.43 94.8% 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 Sun Oct 9 2011 at 20:44:18 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5082 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: SEP 674 has a net charge of -0.4750 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.708636 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): 1.872000 64.37800 ymin,ymax (A): -7.714000 54.61100 zmin,zma (A): -1.135000 59.96300 x,y,z range (A): 62.50600 62.32500 61.09800 scale (grids/A): 1.708636 object centre (A): 33.12500 23.44850 29.41400 number of atom coordinates read : 5082 total number of charged atoms : 4926 net assigned charge : 2.660028 assigned positive charge : 783.5439 centred at (gu) : 85.13342 86.72506 88.44212 assigned negative charge : -780.8895 centred at (gu) : 84.82060 86.64938 88.32280 start vw surface at 0.1800000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 118370 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39513 grid for indexing accessible points = 1.400000 m= 42536 mr = 85923 m= 5613 mr = 30996 m= 207 mr = 3201 m= 4 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9500000 number of dielectric boundary points 46573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 351 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 38065 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) : 0.5695453 object centre at (A) : 33.12500 23.44850 29.41400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1280756E-02 -2.5714859E-03 midg,1,midg; midg,igrid,midg 2.0191742E-02 1.5000274E-02 1,midg,midg; igrid,midg,midg 2.2090692E-03 4.9645077E-02 gauss-seidel spectral radius is 0.9985325 estimated iterations to convergence 207 setup time was (sec) 1.260000 now iterating at: 20:44:20 rms-change max change #iterations 5.172295 199.0610 at 10iterations 2.346610 65.88961 at 20iterations 1.070939 28.37779 at 30iterations 0.4892429 13.73179 at 40iterations 0.2236230 6.103585 at 50iterations 0.1028507 3.015982 at 60iterations 4.7377717E-02 1.219952 at 70iterations 2.2270175E-02 0.5817413 at 80iterations 1.0967515E-02 0.3023567 at 90iterations 5.9200055E-03 0.1606398 at 100iterations 3.6176099E-03 9.9447250E-02 at 110iterations 2.4972046E-03 6.6183090E-02 at 120iterations finished qdiffx linear iterations at : 20:44:30 total time elapsed so far: 11.22000 # loops : 120 mean,max change (kT/e) : 2.4972046E-03 6.6183090E-02 energy calculations done at 11.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.38000 DelPhi exited at 20:44:31 11.385u 0.467s 0:12.12 97.6% 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 20:44:31 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5082 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: SEP 674 has a net charge of -0.4750 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.562954 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): 1.872000 64.37800 ymin,ymax (A): -7.714000 54.61100 zmin,zma (A): -1.135000 59.96300 x,y,z range (A): 62.50600 62.32500 61.09800 scale (grids/A): 2.562954 object centre (A): 33.12500 23.44850 29.41400 number of atom coordinates read : 5082 total number of charged atoms : 4926 net assigned charge : 2.660028 assigned positive charge : 783.5439 centred at (gu) : 82.69974 85.08725 87.66265 assigned negative charge : -780.8895 centred at (gu) : 82.23087 84.97399 87.48417 start vw surface at 0.1800000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 274823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39513 grid for indexing accessible points = 1.400000 m= 140888 mr = 208382 m= 47735 mr = 115737 m= 9630 mr = 37584 m= 992 mr = 6742 m= 26 mr = 539 m= 0 mr = 0 time to grow re-entrant surface = 1.570000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.470000 number of dielectric boundary points 105110 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 2.640000 number of grid points assigned charge 39380 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) : 1.708636 object centre at (A) : 33.12500 23.44850 29.41400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5050668 7.5558767E-02 midg,1,midg; midg,igrid,midg -9.9608198E-02 0.1044231 1,midg,midg; igrid,midg,midg -8.4164254E-03 0.8888317 gauss-seidel spectral radius is 0.9992796 estimated iterations to convergence 294 setup time was (sec) 2.840000 now iterating at: 20:44:34 rms-change max change #iterations 12.92546 421.5394 at 10iterations 7.696293 150.0092 at 20iterations 4.560571 80.23594 at 30iterations 2.690278 55.58512 at 40iterations 1.581955 26.80461 at 50iterations 0.9280294 14.66838 at 60iterations 0.5413297 11.98452 at 70iterations 0.3164324 4.993017 at 80iterations 0.1842608 2.995412 at 90iterations 0.1074502 1.693733 at 100iterations 6.2747061E-02 1.018563 at 110iterations 3.6634102E-02 0.5881195 at 120iterations 2.1582237E-02 0.3299751 at 130iterations 1.2857536E-02 0.2015076 at 140iterations 7.8733237E-03 0.1295166 at 150iterations 5.0393343E-03 8.6081028E-02 at 160iterations 3.4300373E-03 5.2291870E-02 at 170iterations 2.5167535E-03 3.8619995E-02 at 180iterations finished qdiffx linear iterations at : 20:44:52 total time elapsed so far: 20.92000 # loops : 180 mean,max change (kT/e) : 2.5167535E-03 3.8619995E-02 energy calculations done at 20.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.08000 DelPhi exited at 20:44:52 21.089u 0.448s 0:21.83 98.5% 0+0k 0+0io 0pf+0w