Sun Oct 9 13:43:55 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 13:43:55 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: GLM 182 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6902435 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): -44.14100 7.435000 ymin,ymax (A): -36.93500 14.21100 zmin,zma (A): 1.447000 44.71900 x,y,z range (A): 51.57600 51.14600 43.27200 scale (grids/A): 0.6902435 object centre (A): -18.35300 -11.36200 23.08300 number of atom coordinates read : 2366 total number of charged atoms : 2221 net assigned charge : 3.406020 assigned positive charge : 362.0291 centred at (gu) : 90.19985 88.83600 90.84585 assigned negative charge : -358.6236 centred at (gu) : 90.19431 88.68238 90.90321 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7686 nv = 96 ne = 84 npr = 47698 no. pairs analyzed = 47698 no. exposed pairs = 2948 no. arc points = 20493 no. surface atoms = 992 nbur = 1374 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 456 mr = 4304 m= 5 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1883 ## 156 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8622 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5335031E-08 -2.7701739E-09 midg,1,midg; midg,igrid,midg -5.0889454E-08 6.1682208E-08 1,midg,midg; igrid,midg,midg 1.7153683E-08 2.2935152E-08 gauss-seidel spectral radius is 0.9890946 estimated iterations to convergence 78 setup time was (sec) 0.5400000 now iterating at: 13:43:55 rms-change max change #iterations 0.1944755 25.37862 at 10iterations 2.3964239E-02 3.188675 at 20iterations 3.5225512E-03 0.5302963 at 30iterations 8.6326752E-04 0.1314011 at 40iterations 2.8904527E-04 4.5143127E-02 at 50iterations finished qdiffx linear iterations at : 13:43:58 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 2.8904527E-04 4.5143127E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 13:43:59 3.357u 0.149s 0:03.87 90.1% 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 Sun Oct 9 2011 at 13:43:59 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 2.070730 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): -44.14100 7.435000 ymin,ymax (A): -36.93500 14.21100 zmin,zma (A): 1.447000 44.71900 x,y,z range (A): 51.57600 51.14600 43.27200 scale (grids/A): 2.070730 object centre (A): -18.35300 -11.36200 23.08300 number of atom coordinates read : 2366 total number of charged atoms : 2221 net assigned charge : 3.406020 assigned positive charge : 362.0291 centred at (gu) : 90.59929 86.50761 92.53699 assigned negative charge : -358.6236 centred at (gu) : 90.58282 86.04691 92.70943 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20493 grid for indexing accessible points = 1.400000 m= 31734 mr = 57067 m= 5509 mr = 23617 m= 482 mr = 3477 m= 12 mr = 241 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 34821 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17615 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) : 0.6902435 object centre at (A) : -18.35300 -11.36200 23.08300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6581613E-02 1.0025286E-02 midg,1,midg; midg,igrid,midg -4.0360734E-02 6.0534882E-03 1,midg,midg; igrid,midg,midg -9.6331201E-03 3.5777930E-02 gauss-seidel spectral radius is 0.9988144 estimated iterations to convergence 230 setup time was (sec) 0.9000000 now iterating at: 13:44:00 rms-change max change #iterations 4.847010 233.6475 at 10iterations 2.386713 77.84212 at 20iterations 1.174348 38.65742 at 30iterations 0.5828671 16.24265 at 40iterations 0.2875288 8.831273 at 50iterations 0.1417220 4.130182 at 60iterations 7.0253804E-02 2.117979 at 70iterations 3.5085101E-02 1.018505 at 80iterations 1.7657528E-02 0.5106659 at 90iterations 8.9604855E-03 0.2720947 at 100iterations 4.6979766E-03 0.1554012 at 110iterations 2.6020776E-03 9.4650269E-02 at 120iterations finished qdiffx linear iterations at : 13:44:06 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 2.6020776E-03 9.4650269E-02 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 13:44:07 7.574u 0.166s 0:08.06 95.9% 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 Sun Oct 9 2011 at 13:44:07 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: GLM 182 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.106096 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): -44.14100 7.435000 ymin,ymax (A): -36.93500 14.21100 zmin,zma (A): 1.447000 44.71900 x,y,z range (A): 51.57600 51.14600 43.27200 scale (grids/A): 3.106096 object centre (A): -18.35300 -11.36200 23.08300 number of atom coordinates read : 2366 total number of charged atoms : 2221 net assigned charge : 3.406020 assigned positive charge : 362.0291 centred at (gu) : 90.89881 84.76140 93.80542 assigned negative charge : -358.6236 centred at (gu) : 90.87426 84.07030 94.06417 start vw surface at 0.1500000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 187827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20493 grid for indexing accessible points = 1.400000 m= 99772 mr = 137436 m= 38464 mr = 82269 m= 9951 mr = 31095 m= 1821 mr = 7407 m= 223 mr = 1306 m= 5 mr = 131 m= 0 mr = 2 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.940000 number of dielectric boundary points 78417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 17768 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) : 2.070730 object centre at (A) : -18.35300 -11.36200 23.08300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5569463 -4.9400959E-02 midg,1,midg; midg,igrid,midg -0.4568982 0.2072502 1,midg,midg; igrid,midg,midg -0.4076385 0.3032108 gauss-seidel spectral radius is 0.9992946 estimated iterations to convergence 297 setup time was (sec) 2.250000 now iterating at: 13:44:09 rms-change max change #iterations 10.88505 425.5540 at 10iterations 6.461415 161.8072 at 20iterations 3.823079 80.39992 at 30iterations 2.264081 41.35632 at 40iterations 1.335780 22.85815 at 50iterations 0.7865730 14.02498 at 60iterations 0.4603007 7.967626 at 70iterations 0.2706135 4.498718 at 80iterations 0.1585123 2.609859 at 90iterations 9.3037114E-02 1.569435 at 100iterations 5.4591659E-02 0.9140933 at 110iterations 3.2287411E-02 0.5403748 at 120iterations 1.9327523E-02 0.3798370 at 130iterations 1.1770228E-02 0.2265167 at 140iterations 7.4350378E-03 0.1489506 at 150iterations 4.9355379E-03 9.6092224E-02 at 160iterations 3.5078011E-03 7.4157715E-02 at 170iterations 2.6488900E-03 5.3981781E-02 at 180iterations finished qdiffx linear iterations at : 13:44:19 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 2.6488900E-03 5.3981781E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 13:44:20 12.826u 0.183s 0:13.32 97.5% 0+0k 0+0io 0pf+0w