Tue Oct 11 07:33:29 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 Tue Oct 11 2011 at 07:33:29 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3297 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 0.6091717 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): 75.47100 125.3930 ymin,ymax (A): -8.514999 48.89900 zmin,zma (A): -2.270000 56.17000 x,y,z range (A): 49.92200 57.41400 58.44000 scale (grids/A): 0.6091717 object centre (A): 100.4320 20.19200 26.95000 number of atom coordinates read : 3297 total number of charged atoms : 3145 net assigned charge : 0.4000090 assigned positive charge : 495.2106 centred at (gu) : 90.57817 89.56944 89.21240 assigned negative charge : -494.8119 centred at (gu) : 90.68433 89.49158 89.23556 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7922 nv = 96 ne = 84 npr = 69020 no. pairs analyzed = 69020 no. exposed pairs = 3699 no. arc points = 25321 no. surface atoms = 1267 nbur = 2030 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 4656 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 0.4100000 number of dielectric boundary points 3610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2595 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 10018 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0442552E-09 -9.5102215E-10 midg,1,midg; midg,igrid,midg -5.0146731E-09 4.5655835E-09 1,midg,midg; igrid,midg,midg 5.9102523E-09 -7.2172521E-09 gauss-seidel spectral radius is 0.9860986 estimated iterations to convergence 69 setup time was (sec) 0.6800000 now iterating at: 07:33:30 rms-change max change #iterations 0.1305411 20.41972 at 10iterations 1.2136592E-02 1.848247 at 20iterations 1.3673798E-03 0.1724758 at 30iterations 2.6081284E-04 4.0401459E-02 at 40iterations 6.6892746E-05 1.0467529E-02 at 50iterations finished qdiffx linear iterations at : 07:33:33 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 6.6892746E-05 1.0467529E-02 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 07:33:34 4.137u 0.276s 0:05.01 87.8% 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 Tue Oct 11 2011 at 07:33:34 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3297 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 1.827515 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): 75.47100 125.3930 ymin,ymax (A): -8.514999 48.89900 zmin,zma (A): -2.270000 56.17000 x,y,z range (A): 49.92200 57.41400 58.44000 scale (grids/A): 1.827515 object centre (A): 100.4320 20.19200 26.95000 number of atom coordinates read : 3297 total number of charged atoms : 3145 net assigned charge : 0.4000090 assigned positive charge : 495.2106 centred at (gu) : 91.73353 88.70766 87.63617 assigned negative charge : -494.8119 centred at (gu) : 92.05244 88.47423 87.70612 start vw surface at 0.1800000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 87738 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25321 grid for indexing accessible points = 1.400000 m= 30919 mr = 63719 m= 4141 mr = 23347 m= 186 mr = 2525 m= 3 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 3630 time to turn everything in is 0.7600000 number of dielectric boundary points 33325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 24629 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) : 0.6091717 object centre at (A) : 100.4320 20.19200 26.95000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2258338E-03 1.0487802E-02 midg,1,midg; midg,igrid,midg -1.2546973E-02 9.3176095E-03 1,midg,midg; igrid,midg,midg 1.6654292E-02 -1.6376548E-02 gauss-seidel spectral radius is 0.9985809 estimated iterations to convergence 210 setup time was (sec) 1.060000 now iterating at: 07:33:36 rms-change max change #iterations 4.468595 168.9638 at 10iterations 2.064915 74.15327 at 20iterations 0.9521213 30.40984 at 30iterations 0.4426270 13.28246 at 40iterations 0.2044425 6.108394 at 50iterations 9.4412073E-02 2.755178 at 60iterations 4.3780439E-02 1.396453 at 70iterations 2.0270035E-02 0.5919495 at 80iterations 9.3839979E-03 0.2633495 at 90iterations 4.3719490E-03 0.1207409 at 100iterations 2.0512256E-03 5.9860229E-02 at 110iterations 9.6149597E-04 2.9935837E-02 at 120iterations finished qdiffx linear iterations at : 07:33:44 total time elapsed so far: 9.410000 # loops : 120 mean,max change (kT/e) : 9.6149597E-04 2.9935837E-02 energy calculations done at 9.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 07:33:45 9.588u 0.298s 0:10.37 95.1% 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 07:33:45 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3297 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 2.741273 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): 75.47100 125.3930 ymin,ymax (A): -8.514999 48.89900 zmin,zma (A): -2.270000 56.17000 x,y,z range (A): 49.92200 57.41400 58.44000 scale (grids/A): 2.741273 object centre (A): 100.4320 20.19200 26.95000 number of atom coordinates read : 3297 total number of charged atoms : 3145 net assigned charge : 0.4000090 assigned positive charge : 495.2106 centred at (gu) : 92.60007 88.06136 86.45401 assigned negative charge : -494.8119 centred at (gu) : 93.07854 87.71124 86.55907 start vw surface at 0.1600000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 203693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25321 grid for indexing accessible points = 1.400000 m= 103163 mr = 154055 m= 34432 mr = 86249 m= 7185 mr = 27923 m= 854 mr = 5351 m= 45 mr = 569 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 12063 time to turn everything in is 1.910000 number of dielectric boundary points 75210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 25158 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) : 1.827515 object centre at (A) : 100.4320 20.19200 26.95000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1405502 0.1591987 midg,1,midg; midg,igrid,midg 1.9018272E-02 9.1880120E-02 1,midg,midg; igrid,midg,midg 0.1818152 -0.1945039 gauss-seidel spectral radius is 0.9992498 estimated iterations to convergence 288 setup time was (sec) 2.240000 now iterating at: 07:33:47 rms-change max change #iterations 10.61502 395.9005 at 10iterations 6.176096 139.8915 at 20iterations 3.570925 66.98591 at 30iterations 2.058226 36.50338 at 40iterations 1.185790 21.85373 at 50iterations 0.6814889 11.70319 at 60iterations 0.3909796 7.309433 at 70iterations 0.2244729 3.967194 at 80iterations 0.1286894 2.300369 at 90iterations 7.3900528E-02 1.324207 at 100iterations 4.2353619E-02 0.7449455 at 110iterations 2.4310522E-02 0.3943977 at 120iterations 1.3932672E-02 0.2698517 at 130iterations 8.0184881E-03 0.1328125 at 140iterations 4.6247472E-03 8.4779739E-02 at 150iterations 2.6820232E-03 4.6406269E-02 at 160iterations 1.5696626E-03 2.6777267E-02 at 170iterations 9.3261542E-04 1.6857147E-02 at 180iterations finished qdiffx linear iterations at : 07:34:01 total time elapsed so far: 16.08000 # loops : 180 mean,max change (kT/e) : 9.3261542E-04 1.6857147E-02 energy calculations done at 16.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.26000 DelPhi exited at 07:34:02 16.261u 0.315s 0:17.23 96.1% 0+0k 0+0io 0pf+0w