Sat Oct 8 23:59:43 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 Sat Oct 8 2011 at 23:59:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2496 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5857865 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): -13.52000 40.29800 ymin,ymax (A): -31.18500 29.58800 zmin,zma (A): -9.488000 32.69200 x,y,z range (A): 53.81800 60.77300 42.18000 scale (grids/A): 0.5857865 object centre (A): 13.38900 -0.7985001 11.60200 number of atom coordinates read : 2496 total number of charged atoms : 2360 net assigned charge : 11.50002 assigned positive charge : 362.0070 centred at (gu) : 89.95554 90.19609 90.57320 assigned negative charge : -350.5078 centred at (gu) : 89.93159 90.21333 90.52761 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5722 nv = 96 ne = 84 npr = 49716 no. pairs analyzed = 49716 no. exposed pairs = 3307 no. arc points = 23806 no. surface atoms = 1099 nbur = 1397 mkacc time = 9.9999994E-02 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 = 1.484000 m= 288 mr = 2903 m= 0 mr = 20 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2800000 number of dielectric boundary points 3087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2291 ## 261 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7144 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8534276E-09 4.5763437E-09 midg,1,midg; midg,igrid,midg 3.2764644E-09 2.8211538E-09 1,midg,midg; igrid,midg,midg 2.5841931E-09 3.5290630E-09 gauss-seidel spectral radius is 0.9849229 estimated iterations to convergence 67 setup time was (sec) 0.4900000 now iterating at: 23:59:43 rms-change max change #iterations 8.9325748E-02 18.48146 at 10iterations 7.2196256E-03 1.212358 at 20iterations 7.1552361E-04 0.1192322 at 30iterations 1.5541834E-04 3.2402039E-02 at 40iterations 5.3135445E-05 1.1588097E-02 at 50iterations finished qdiffx linear iterations at : 23:59:46 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 5.3135445E-05 1.1588097E-02 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 23:59:47 3.091u 0.155s 0:03.70 87.5% 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 23:59:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2496 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.757359 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): -13.52000 40.29800 ymin,ymax (A): -31.18500 29.58800 zmin,zma (A): -9.488000 32.69200 x,y,z range (A): 53.81800 60.77300 42.18000 scale (grids/A): 1.757359 object centre (A): 13.38900 -0.7985001 11.60200 number of atom coordinates read : 2496 total number of charged atoms : 2360 net assigned charge : 11.50002 assigned positive charge : 362.0070 centred at (gu) : 89.86610 90.58794 91.71912 assigned negative charge : -350.5078 centred at (gu) : 89.79463 90.63993 91.58253 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 62305 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23806 grid for indexing accessible points = 1.400000 m= 21111 mr = 41285 m= 2883 mr = 14851 m= 114 mr = 1599 m= 0 mr = 18 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1493 time to turn everything in is 0.4700000 number of dielectric boundary points 28660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 241 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 18376 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) : 0.5857865 object centre at (A) : 13.38900 -0.7985001 11.60200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7665253E-03 1.3528928E-02 midg,1,midg; midg,igrid,midg 2.9296735E-02 1.4515262E-02 1,midg,midg; igrid,midg,midg 2.4643652E-02 2.6223741E-02 gauss-seidel spectral radius is 0.9984018 estimated iterations to convergence 198 setup time was (sec) 0.7500000 now iterating at: 23:59:48 rms-change max change #iterations 3.389105 157.1862 at 10iterations 1.482108 60.88591 at 20iterations 0.6519294 25.12289 at 30iterations 0.2876016 12.17389 at 40iterations 0.1259238 4.525496 at 50iterations 5.5850822E-02 2.060330 at 60iterations 2.4520669E-02 0.8587875 at 70iterations 1.0775948E-02 0.3950672 at 80iterations 4.7705057E-03 0.1907558 at 90iterations 2.1238036E-03 7.5321674E-02 at 100iterations 9.6469815E-04 3.4322739E-02 at 110iterations 4.4905258E-04 2.1286011E-02 at 120iterations finished qdiffx linear iterations at : 23:59:54 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 4.4905258E-04 2.1286011E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 23:59:55 7.768u 0.220s 0:08.40 95.0% 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 23:59:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2496 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.636039 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): -13.52000 40.29800 ymin,ymax (A): -31.18500 29.58800 zmin,zma (A): -9.488000 32.69200 x,y,z range (A): 53.81800 60.77300 42.18000 scale (grids/A): 2.636039 object centre (A): 13.38900 -0.7985001 11.60200 number of atom coordinates read : 2496 total number of charged atoms : 2360 net assigned charge : 11.50002 assigned positive charge : 362.0070 centred at (gu) : 89.79904 90.88172 92.57862 assigned negative charge : -350.5078 centred at (gu) : 89.69192 90.95995 92.37368 start vw surface at 0.1300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 144080 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23806 grid for indexing accessible points = 1.400000 m= 69581 mr = 100822 m= 23105 mr = 55204 m= 4864 mr = 17924 m= 538 mr = 3369 m= 14 mr = 302 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 4849 time to turn everything in is 1.120000 number of dielectric boundary points 64561 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 18879 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) : 1.757359 object centre at (A) : 13.38900 -0.7985001 11.60200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6159810E-03 0.1577805 midg,1,midg; midg,igrid,midg 0.5128464 0.2801269 1,midg,midg; igrid,midg,midg 0.3011287 0.3465659 gauss-seidel spectral radius is 0.9991971 estimated iterations to convergence 279 setup time was (sec) 1.450000 now iterating at: 23:59:57 rms-change max change #iterations 8.504485 329.3212 at 10iterations 4.895859 130.0144 at 20iterations 2.804192 74.25549 at 30iterations 1.598268 42.87273 at 40iterations 0.9078902 22.43483 at 50iterations 0.5153028 12.72062 at 60iterations 0.2909042 6.762013 at 70iterations 0.1642579 3.798886 at 80iterations 9.2678994E-02 2.109028 at 90iterations 5.2269295E-02 1.118715 at 100iterations 2.9398803E-02 0.5919342 at 110iterations 1.6545765E-02 0.3388443 at 120iterations 9.3283001E-03 0.2006302 at 130iterations 5.2327956E-03 0.1052017 at 140iterations 2.9436932E-03 6.2137127E-02 at 150iterations 1.6544370E-03 3.5324097E-02 at 160iterations 9.2809839E-04 2.2267938E-02 at 170iterations 5.2125775E-04 1.0568619E-02 at 180iterations finished qdiffx linear iterations at : 00:00:08 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 5.2125775E-04 1.0568619E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 00:00:08 12.685u 0.253s 0:13.21 97.8% 0+0k 0+0io 0pf+0w