Sun Oct 9 17:26:59 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 17:26:59 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4923 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5632555 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): 3.226000 64.45500 ymin,ymax (A): -8.618999 53.45900 zmin,zma (A): -1.215000 61.98900 x,y,z range (A): 61.22900 62.07800 63.20400 scale (grids/A): 0.5632555 object centre (A): 33.84050 22.42000 30.38700 number of atom coordinates read : 4923 total number of charged atoms : 4783 net assigned charge : 1.635044 assigned positive charge : 759.6832 centred at (gu) : 88.33294 89.22309 89.10105 assigned negative charge : -758.0535 centred at (gu) : 88.21940 89.23821 89.07101 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 10283 nv = 96 ne = 84 npr = 99087 no. pairs analyzed = 99087 no. exposed pairs = 5911 no. arc points = 39722 no. surface atoms = 2015 nbur = 2908 mkacc time = 0.1700000 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= 525 mr = 5920 m= 3 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4016 ## 416 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 13419 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9057186E-10 7.0544509E-10 midg,1,midg; midg,igrid,midg 6.7938249E-10 -6.0322324E-11 1,midg,midg; igrid,midg,midg -3.3041037E-09 1.7428012E-09 gauss-seidel spectral radius is 0.9838837 estimated iterations to convergence 65 setup time was (sec) 0.5200000 now iterating at: 17:27:00 rms-change max change #iterations 0.1175676 15.77879 at 10iterations 1.0568622E-02 1.528580 at 20iterations 2.6177610E-03 0.3003845 at 30iterations 1.1977919E-03 0.1286545 at 40iterations 5.8028870E-04 6.7039013E-02 at 50iterations finished qdiffx linear iterations at : 17:27:03 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 5.8028870E-04 6.7039013E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 17:27:03 3.567u 0.177s 0:04.06 91.8% 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 17:27:03 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4923 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.689767 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): 3.226000 64.45500 ymin,ymax (A): -8.618999 53.45900 zmin,zma (A): -1.215000 61.98900 x,y,z range (A): 61.22900 62.07800 63.20400 scale (grids/A): 1.689767 object centre (A): 33.84050 22.42000 30.38700 number of atom coordinates read : 4923 total number of charged atoms : 4783 net assigned charge : 1.635044 assigned positive charge : 759.6832 centred at (gu) : 84.99734 87.66802 87.30201 assigned negative charge : -758.0535 centred at (gu) : 84.65814 87.71459 87.21284 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 114490 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39722 grid for indexing accessible points = 1.400000 m= 40824 mr = 82960 m= 5226 mr = 29566 m= 192 mr = 2866 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 45313 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 336 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 36912 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) : 0.5632555 object centre at (A) : 33.84050 22.42000 30.38700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4949009E-02 -2.7542090E-02 midg,1,midg; midg,igrid,midg 1.7754668E-02 1.0891856E-02 1,midg,midg; igrid,midg,midg -1.7466750E-02 4.0332980E-02 gauss-seidel spectral radius is 0.9984881 estimated iterations to convergence 204 setup time was (sec) 0.8000000 now iterating at: 17:27:04 rms-change max change #iterations 4.952191 222.6503 at 10iterations 2.222831 84.91010 at 20iterations 1.000697 30.06125 at 30iterations 0.4519020 13.44707 at 40iterations 0.2038494 5.521043 at 50iterations 9.2522681E-02 2.533568 at 60iterations 4.2131688E-02 1.081078 at 70iterations 1.9560240E-02 0.5461044 at 80iterations 9.4984090E-03 0.2642899 at 90iterations 5.0985548E-03 0.1495972 at 100iterations 3.1367152E-03 8.6425781E-02 at 110iterations 2.1913585E-03 5.3205490E-02 at 120iterations finished qdiffx linear iterations at : 17:27:12 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 2.1913585E-03 5.3205490E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 17:27:12 8.217u 0.187s 0:08.67 96.7% 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 17:27:12 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4923 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.534650 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): 3.226000 64.45500 ymin,ymax (A): -8.618999 53.45900 zmin,zma (A): -1.215000 61.98900 x,y,z range (A): 61.22900 62.07800 63.20400 scale (grids/A): 2.534650 object centre (A): 33.84050 22.42000 30.38700 number of atom coordinates read : 4923 total number of charged atoms : 4783 net assigned charge : 1.635044 assigned positive charge : 759.6832 centred at (gu) : 82.49556 86.50175 85.95259 assigned negative charge : -758.0535 centred at (gu) : 81.98714 86.57188 85.81918 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 265623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39722 grid for indexing accessible points = 1.400000 m= 136337 mr = 201309 m= 44653 mr = 111283 m= 8579 mr = 34850 m= 761 mr = 5888 m= 22 mr = 401 m= 0 mr = 2 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.400000 number of dielectric boundary points 102242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 38240 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) : 1.689767 object centre at (A) : 33.84050 22.42000 30.38700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4399897 -0.6973910 midg,1,midg; midg,igrid,midg -1.4473376E-02 9.5372768E-03 1,midg,midg; igrid,midg,midg -0.3564876 0.6188306 gauss-seidel spectral radius is 0.9992677 estimated iterations to convergence 292 setup time was (sec) 1.660000 now iterating at: 17:27:14 rms-change max change #iterations 12.47217 307.0939 at 10iterations 7.404594 164.1740 at 20iterations 4.371202 94.33694 at 30iterations 2.566948 46.27774 at 40iterations 1.504051 25.18678 at 50iterations 0.8774117 15.22309 at 60iterations 0.5104879 8.669132 at 70iterations 0.2970114 5.193312 at 80iterations 0.1727587 2.893580 at 90iterations 0.1001286 1.650249 at 100iterations 5.8189310E-02 0.9853821 at 110iterations 3.3892147E-02 0.5227585 at 120iterations 1.9924022E-02 0.3259048 at 130iterations 1.1895679E-02 0.1936646 at 140iterations 7.3301094E-03 0.1233940 at 150iterations 4.7570085E-03 8.2702637E-02 at 160iterations 3.3114399E-03 5.6855679E-02 at 170iterations 2.4888832E-03 3.6884785E-02 at 180iterations finished qdiffx linear iterations at : 17:27:26 total time elapsed so far: 13.64000 # loops : 180 mean,max change (kT/e) : 2.4888832E-03 3.6884785E-02 energy calculations done at 13.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.77000 DelPhi exited at 17:27:26 13.775u 0.223s 0:14.32 97.6% 0+0k 0+0io 0pf+0w