Mon Oct 10 19:37:20 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 Mon Oct 10 2011 at 19:37:20 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 = 2633 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6024708 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): -30.78200 20.21000 ymin,ymax (A): -61.78100 -2.691000 zmin,zma (A): 7.879000 63.13100 x,y,z range (A): 50.99200 59.09000 55.25200 scale (grids/A): 0.6024708 object centre (A): -5.285999 -32.23600 35.50500 number of atom coordinates read : 2633 total number of charged atoms : 2495 net assigned charge : 8.000035 assigned positive charge : 388.5397 centred at (gu) : 91.09084 87.55891 87.57214 assigned negative charge : -380.5409 centred at (gu) : 91.04633 87.51921 87.57352 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6424 nv = 96 ne = 84 npr = 51631 no. pairs analyzed = 51631 no. exposed pairs = 3683 no. arc points = 25661 no. surface atoms = 1244 nbur = 1389 mkacc time = 8.9999996E-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 = 1.456000 m= 361 mr = 3186 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2599 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7974 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3906640E-09 2.1483053E-09 midg,1,midg; midg,igrid,midg 3.6348389E-09 3.0353187E-09 1,midg,midg; igrid,midg,midg 1.5764635E-09 6.8391022E-09 gauss-seidel spectral radius is 0.9857522 estimated iterations to convergence 69 setup time was (sec) 0.4000000 now iterating at: 19:37:21 rms-change max change #iterations 0.1096912 17.38512 at 10iterations 9.6646594E-03 1.472211 at 20iterations 1.0580752E-03 0.1631165 at 30iterations 2.0621042E-04 3.0447006E-02 at 40iterations 5.8845562E-05 8.4095001E-03 at 50iterations finished qdiffx linear iterations at : 19:37:24 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 5.8845562E-05 8.4095001E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 19:37:25 3.443u 0.160s 0:04.31 83.5% 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 Mon Oct 10 2011 at 19:37:25 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 = 2633 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.807412 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): -30.78200 20.21000 ymin,ymax (A): -61.78100 -2.691000 zmin,zma (A): 7.879000 63.13100 x,y,z range (A): 50.99200 59.09000 55.25200 scale (grids/A): 1.807412 object centre (A): -5.285999 -32.23600 35.50500 number of atom coordinates read : 2633 total number of charged atoms : 2495 net assigned charge : 8.000035 assigned positive charge : 388.5397 centred at (gu) : 93.27170 82.67599 82.71592 assigned negative charge : -380.5409 centred at (gu) : 93.13893 82.55772 82.72070 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 70291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25661 grid for indexing accessible points = 1.400000 m= 23541 mr = 46319 m= 3305 mr = 15988 m= 150 mr = 1768 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 33189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 193 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19501 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) : 0.6024708 object centre at (A) : -5.285999 -32.23600 35.50500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3938005E-03 1.4528170E-02 midg,1,midg; midg,igrid,midg 3.2677948E-02 2.7516257E-02 1,midg,midg; igrid,midg,midg 2.3596106E-02 1.8553045E-02 gauss-seidel spectral radius is 0.9984961 estimated iterations to convergence 205 setup time was (sec) 0.5900000 now iterating at: 19:37:25 rms-change max change #iterations 3.818031 183.0331 at 10iterations 1.701696 69.14591 at 20iterations 0.7669721 27.76545 at 30iterations 0.3451898 11.82428 at 40iterations 0.1555457 5.007434 at 50iterations 6.9990367E-02 2.438416 at 60iterations 3.1637236E-02 1.174576 at 70iterations 1.4298770E-02 0.5047302 at 80iterations 6.5002656E-03 0.2187500 at 90iterations 2.9574365E-03 9.8037720E-02 at 100iterations 1.3806846E-03 5.1403046E-02 at 110iterations 6.6234573E-04 2.2583008E-02 at 120iterations finished qdiffx linear iterations at : 19:37:33 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 6.6234573E-04 2.2583008E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 19:37:33 7.899u 0.213s 0:08.62 93.9% 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 Mon Oct 10 2011 at 19:37:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2633 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.711118 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): -30.78200 20.21000 ymin,ymax (A): -61.78100 -2.691000 zmin,zma (A): 7.879000 63.13100 x,y,z range (A): 50.99200 59.09000 55.25200 scale (grids/A): 2.711118 object centre (A): -5.285999 -32.23600 35.50500 number of atom coordinates read : 2633 total number of charged atoms : 2495 net assigned charge : 8.000035 assigned positive charge : 388.5397 centred at (gu) : 94.90741 79.01402 79.07367 assigned negative charge : -380.5409 centred at (gu) : 94.70837 78.83653 79.08120 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 162750 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25661 grid for indexing accessible points = 1.400000 m= 76765 mr = 113389 m= 26027 mr = 59608 m= 5608 mr = 19804 m= 671 mr = 3844 m= 32 mr = 381 m= 0 mr = 2 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8800000 number of dielectric boundary points 74825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 19954 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) : 1.807412 object centre at (A) : -5.285999 -32.23600 35.50500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9336023E-02 0.2490800 midg,1,midg; midg,igrid,midg 0.5497741 0.3335668 1,midg,midg; igrid,midg,midg 0.4527248 0.1373079 gauss-seidel spectral radius is 0.9992338 estimated iterations to convergence 285 setup time was (sec) 1.120000 now iterating at: 19:37:35 rms-change max change #iterations 9.534475 312.4183 at 10iterations 5.671577 168.6936 at 20iterations 3.327261 79.04759 at 30iterations 1.941935 41.72700 at 40iterations 1.126528 26.31523 at 50iterations 0.6492454 13.78163 at 60iterations 0.3735209 9.097418 at 70iterations 0.2146007 4.589204 at 80iterations 0.1229524 2.567021 at 90iterations 7.0468172E-02 1.456944 at 100iterations 4.0297363E-02 0.8766966 at 110iterations 2.3062397E-02 0.4818316 at 120iterations 1.3245840E-02 0.3526306 at 130iterations 7.6287398E-03 0.1551819 at 140iterations 4.4179675E-03 8.4867477E-02 at 150iterations 2.5923655E-03 5.0149918E-02 at 160iterations 1.5543092E-03 3.3899307E-02 at 170iterations 9.6600648E-04 2.0942688E-02 at 180iterations finished qdiffx linear iterations at : 19:37:46 total time elapsed so far: 12.53000 # loops : 180 mean,max change (kT/e) : 9.6600648E-04 2.0942688E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.67000 DelPhi exited at 19:37:47 12.670u 0.210s 0:13.44 95.8% 0+0k 0+0io 0pf+0w