Sat Oct 8 11:37:33 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 11:37:33 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 = 4876 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5448090 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): 7.707000 73.05099 ymin,ymax (A): 4.522000 66.16300 zmin,zma (A): 9.438999 74.52500 x,y,z range (A): 65.34399 61.64100 65.08600 scale (grids/A): 0.5448090 object centre (A): 40.37900 35.34250 41.98200 number of atom coordinates read : 4876 total number of charged atoms : 4711 net assigned charge : 4.6312809E-05 assigned positive charge : 732.9460 centred at (gu) : 90.35138 90.20627 90.58926 assigned negative charge : -732.9503 centred at (gu) : 90.24885 90.23531 90.65694 start vw surface at 0.2600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 9036 nv = 96 ne = 84 npr = 101820 no. pairs analyzed = 101820 no. exposed pairs = 5784 no. arc points = 39969 no. surface atoms = 1953 nbur = 2923 mkacc time = 0.3000000 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 = 1.568000 m= 367 mr = 4894 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 4494 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4098 ## 503 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 12226 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0856231E-10 -8.2913632E-10 midg,1,midg; midg,igrid,midg 2.8985425E-10 -3.2010067E-10 1,midg,midg; igrid,midg,midg -9.9548159E-10 1.1622983E-09 gauss-seidel spectral radius is 0.9827650 estimated iterations to convergence 63 setup time was (sec) 0.8800000 now iterating at: 11:37:34 rms-change max change #iterations 9.2837125E-02 11.54531 at 10iterations 8.2256403E-03 1.517502 at 20iterations 1.6856522E-03 0.3586884 at 30iterations 4.9809774E-04 0.1002884 at 40iterations 1.6200275E-04 2.9487610E-02 at 50iterations finished qdiffx linear iterations at : 11:37:37 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 1.6200275E-04 2.9487610E-02 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 11:37:38 4.237u 0.154s 0:04.83 90.6% 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 Sat Oct 8 2011 at 11:37:38 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 = 4876 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.634427 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): 7.707000 73.05099 ymin,ymax (A): 4.522000 66.16300 zmin,zma (A): 9.438999 74.52500 x,y,z range (A): 65.34399 61.64100 65.08600 scale (grids/A): 1.634427 object centre (A): 40.37900 35.34250 41.98200 number of atom coordinates read : 4876 total number of charged atoms : 4711 net assigned charge : 4.6312809E-05 assigned positive charge : 732.9460 centred at (gu) : 91.05270 90.61737 91.76630 assigned negative charge : -732.9503 centred at (gu) : 90.74614 90.70547 91.97037 start vw surface at 0.2500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 101883 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39969 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 31987 mr = 71961 m= 3347 mr = 22001 m= 79 mr = 1669 m= 0 mr = 6 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 317 time to turn everything in is 0.9100000 number of dielectric boundary points 41659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 464 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 36042 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) : 0.5448090 object centre at (A) : 40.37900 35.34250 41.98200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6436947E-02 -1.5066955E-03 midg,1,midg; midg,igrid,midg -6.3216761E-03 -7.1605295E-03 1,midg,midg; igrid,midg,midg -1.2395522E-02 9.8019140E-03 gauss-seidel spectral radius is 0.9983752 estimated iterations to convergence 197 setup time was (sec) 1.270000 now iterating at: 11:37:39 rms-change max change #iterations 4.442245 225.7998 at 10iterations 1.937369 58.44618 at 20iterations 0.8501256 23.76445 at 30iterations 0.3722270 10.31416 at 40iterations 0.1631722 4.578522 at 50iterations 7.1668543E-02 2.068417 at 60iterations 3.1761494E-02 0.9281082 at 70iterations 1.4108836E-02 0.4204674 at 80iterations 6.4352644E-03 0.2193031 at 90iterations 3.0298890E-03 0.1046600 at 100iterations 1.4966496E-03 5.2474976E-02 at 110iterations 8.1707450E-04 2.9876709E-02 at 120iterations finished qdiffx linear iterations at : 11:37:47 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 8.1707450E-04 2.9876709E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.580000 DelPhi exited at 11:37:48 9.582u 0.256s 0:10.39 94.6% 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 Sat Oct 8 2011 at 11:37:48 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 = 4876 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.451641 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): 7.707000 73.05099 ymin,ymax (A): 4.522000 66.16300 zmin,zma (A): 9.438999 74.52500 x,y,z range (A): 65.34399 61.64100 65.08600 scale (grids/A): 2.451641 object centre (A): 40.37900 35.34250 41.98200 number of atom coordinates read : 4876 total number of charged atoms : 4711 net assigned charge : 4.6312809E-05 assigned positive charge : 732.9460 centred at (gu) : 91.57880 90.92574 92.64909 assigned negative charge : -732.9503 centred at (gu) : 91.11906 91.05808 92.95544 start vw surface at 0.2500000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 237374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39969 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 110326 mr = 175886 m= 31852 mr = 87680 m= 5078 mr = 24040 m= 337 mr = 3301 m= 6 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 1.320000 no. cavity mid-points inaccessible to solvent = 1010 time to turn everything in is 2.210000 number of dielectric boundary points 93940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 37650 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) : 1.634427 object centre at (A) : 40.37900 35.34250 41.98200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3786946 -0.2251494 midg,1,midg; midg,igrid,midg -0.1004953 -0.1477848 1,midg,midg; igrid,midg,midg -0.3360444 -5.8346651E-03 gauss-seidel spectral radius is 0.9992390 estimated iterations to convergence 286 setup time was (sec) 2.590000 now iterating at: 11:37:51 rms-change max change #iterations 11.55093 305.7366 at 10iterations 6.842340 150.0679 at 20iterations 4.034740 83.99628 at 30iterations 2.359285 48.45722 at 40iterations 1.374292 25.68731 at 50iterations 0.7983269 15.46325 at 60iterations 0.4627630 8.391313 at 70iterations 0.2677583 4.455334 at 80iterations 0.1545590 2.697945 at 90iterations 8.9456461E-02 1.655930 at 100iterations 5.1580124E-02 0.8706608 at 110iterations 2.9681306E-02 0.5431595 at 120iterations 1.7176140E-02 0.3116047 at 130iterations 9.9825384E-03 0.1805363 at 140iterations 5.8393558E-03 0.1023893 at 150iterations 3.4673042E-03 6.1523438E-02 at 160iterations 2.1071774E-03 4.3014526E-02 at 170iterations 1.3288404E-03 2.6443481E-02 at 180iterations finished qdiffx linear iterations at : 11:38:04 total time elapsed so far: 15.28000 # loops : 180 mean,max change (kT/e) : 1.3288404E-03 2.6443481E-02 energy calculations done at 15.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.51000 DelPhi exited at 11:38:04 15.515u 0.216s 0:16.04 98.0% 0+0k 0+0io 0pf+0w