Tue Oct 11 06:38:37 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 Tue Oct 11 2011 at 06:38:37 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2046 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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: 0.7007874 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): -20.23600 24.50400 ymin,ymax (A): -26.67100 10.64800 zmin,zma (A): -14.12400 36.67600 x,y,z range (A): 44.74000 37.31900 50.80000 scale (grids/A): 0.7007874 object centre (A): 2.134000 -8.011499 11.27600 number of atom coordinates read : 2046 total number of charged atoms : 1931 net assigned charge : 6.945010 assigned positive charge : 314.4191 centred at (gu) : 89.75383 90.90317 89.29803 assigned negative charge : -307.4741 centred at (gu) : 89.57220 90.88939 89.27888 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6820 nv = 96 ne = 84 npr = 40916 no. pairs analyzed = 40916 no. exposed pairs = 2474 no. arc points = 17177 no. surface atoms = 844 nbur = 1202 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 443 mr = 3909 m= 2 mr = 69 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 0.2700000 number of dielectric boundary points 3287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1575 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7651 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8157258E-08 5.0954228E-08 midg,1,midg; midg,igrid,midg 3.7542300E-08 6.6599931E-08 1,midg,midg; igrid,midg,midg -2.8834823E-08 1.1907991E-07 gauss-seidel spectral radius is 0.9893840 estimated iterations to convergence 79 setup time was (sec) 0.5000000 now iterating at: 06:38:37 rms-change max change #iterations 0.1925699 25.57139 at 10iterations 2.3897022E-02 3.333228 at 20iterations 3.0625581E-03 0.4118655 at 30iterations 4.5355540E-04 6.5622330E-02 at 40iterations 9.4529700E-05 1.4110565E-02 at 50iterations finished qdiffx linear iterations at : 06:38:40 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 9.4529700E-05 1.4110565E-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) 3.370000 DelPhi exited at 06:38:41 3.371u 0.174s 0:03.83 92.4% 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 06:38:41 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2046 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.102362 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): -20.23600 24.50400 ymin,ymax (A): -26.67100 10.64800 zmin,zma (A): -14.12400 36.67600 x,y,z range (A): 44.74000 37.31900 50.80000 scale (grids/A): 2.102362 object centre (A): 2.134000 -8.011499 11.27600 number of atom coordinates read : 2046 total number of charged atoms : 1931 net assigned charge : 6.945010 assigned positive charge : 314.4191 centred at (gu) : 89.26139 92.70942 87.89395 assigned negative charge : -307.4741 centred at (gu) : 88.71674 92.66830 87.83679 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72326 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17177 grid for indexing accessible points = 1.400000 m= 28549 mr = 51364 m= 5360 mr = 21468 m= 480 mr = 3584 m= 6 mr = 246 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 30059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 15323 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) : 0.7007874 object centre at (A) : 2.134000 -8.011499 11.27600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6174358E-02 4.3162655E-02 midg,1,midg; midg,igrid,midg 4.1950899E-03 3.2803334E-02 1,midg,midg; igrid,midg,midg 5.7770698E-03 3.5185248E-02 gauss-seidel spectral radius is 0.9988078 estimated iterations to convergence 229 setup time was (sec) 0.8500000 now iterating at: 06:38:42 rms-change max change #iterations 4.454128 179.2079 at 10iterations 2.195840 71.53090 at 20iterations 1.079183 33.71082 at 30iterations 0.5337576 17.71097 at 40iterations 0.2629509 8.160192 at 50iterations 0.1305555 4.222437 at 60iterations 6.4092524E-02 2.058208 at 70iterations 3.1822186E-02 1.038784 at 80iterations 1.5779750E-02 0.6037197 at 90iterations 7.8451997E-03 0.2334051 at 100iterations 3.9262669E-03 0.1285439 at 110iterations 1.9972562E-03 6.2698364E-02 at 120iterations finished qdiffx linear iterations at : 06:38:48 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 1.9972562E-03 6.2698364E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 06:38:49 7.727u 0.204s 0:08.23 96.2% 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 06:38:49 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2046 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.153543 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): -20.23600 24.50400 ymin,ymax (A): -26.67100 10.64800 zmin,zma (A): -14.12400 36.67600 x,y,z range (A): 44.74000 37.31900 50.80000 scale (grids/A): 3.153543 object centre (A): 2.134000 -8.011499 11.27600 number of atom coordinates read : 2046 total number of charged atoms : 1931 net assigned charge : 6.945010 assigned positive charge : 314.4191 centred at (gu) : 88.89211 94.06419 86.84082 assigned negative charge : -307.4741 centred at (gu) : 88.07510 94.00239 86.75524 start vw surface at 0.1300000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 166834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17177 grid for indexing accessible points = 1.400000 m= 89668 mr = 123536 m= 35717 mr = 74549 m= 10318 mr = 29270 m= 1967 mr = 7991 m= 178 mr = 1442 m= 5 mr = 97 m= 0 mr = 2 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.760000 number of dielectric boundary points 67800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 15448 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) : 2.102362 object centre at (A) : 2.134000 -8.011499 11.27600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6291173 0.3578558 midg,1,midg; midg,igrid,midg 1.9648999E-02 0.2708519 1,midg,midg; igrid,midg,midg 0.1609834 0.2746234 gauss-seidel spectral radius is 0.9992892 estimated iterations to convergence 296 setup time was (sec) 2.080000 now iterating at: 06:38:51 rms-change max change #iterations 10.09129 342.6777 at 10iterations 5.943081 131.7660 at 20iterations 3.498641 79.50456 at 30iterations 2.055422 41.21280 at 40iterations 1.207216 25.29144 at 50iterations 0.7084450 12.57448 at 60iterations 0.4132773 7.955300 at 70iterations 0.2417084 4.662765 at 80iterations 0.1410231 2.909445 at 90iterations 8.2695812E-02 1.603627 at 100iterations 4.8429891E-02 1.116939 at 110iterations 2.8481606E-02 0.5148621 at 120iterations 1.6830642E-02 0.3344040 at 130iterations 1.0036941E-02 0.1884460 at 140iterations 6.1303293E-03 0.1152344 at 150iterations 3.8364225E-03 7.2170258E-02 at 160iterations 2.5222483E-03 5.2860260E-02 at 170iterations 1.7388595E-03 3.5392761E-02 at 180iterations finished qdiffx linear iterations at : 06:39:02 total time elapsed so far: 13.43000 # loops : 180 mean,max change (kT/e) : 1.7388595E-03 3.5392761E-02 energy calculations done at 13.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.62000 DelPhi exited at 06:39:03 13.625u 0.207s 0:14.10 98.0% 0+0k 0+0io 0pf+0w