Sun Oct 9 07:09:58 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 Sun Oct 9 2011 at 07:09:58 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 0.7109620 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): -21.88900 24.78300 ymin,ymax (A): -26.23400 23.83900 zmin,zma (A): -13.27900 35.39800 x,y,z range (A): 46.67200 50.07300 48.67700 scale (grids/A): 0.7109620 object centre (A): 1.447001 -1.197499 11.05950 number of atom coordinates read : 2011 total number of charged atoms : 1871 net assigned charge : -0.9999837 assigned positive charge : 302.2589 centred at (gu) : 89.88132 90.08784 89.76137 assigned negative charge : -303.2591 centred at (gu) : 90.03898 90.05787 89.83012 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6879 nv = 96 ne = 84 npr = 42771 no. pairs analyzed = 42771 no. exposed pairs = 2381 no. arc points = 17233 no. surface atoms = 808 nbur = 1203 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 3932 m= 7 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3000000 number of dielectric boundary points 3337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1581 ## 128 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7653 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7511048E-08 -4.3228439E-08 midg,1,midg; midg,igrid,midg -2.4508198E-08 6.3557715E-09 1,midg,midg; igrid,midg,midg 7.3127190E-08 -9.0433609E-08 gauss-seidel spectral radius is 0.9896841 estimated iterations to convergence 80 setup time was (sec) 0.5700000 now iterating at: 07:09:59 rms-change max change #iterations 0.2035955 37.30565 at 10iterations 2.5330272E-02 3.806240 at 20iterations 3.1088011E-03 0.4560795 at 30iterations 3.9342165E-04 5.7005525E-02 at 40iterations 4.8373269E-05 6.6337585E-03 at 50iterations finished qdiffx linear iterations at : 07:10:03 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 4.8373269E-05 6.6337585E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 07:10:03 4.022u 0.251s 0:04.55 93.8% 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 07:10:03 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 2.132886 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): -21.88900 24.78300 ymin,ymax (A): -26.23400 23.83900 zmin,zma (A): -13.27900 35.39800 x,y,z range (A): 46.67200 50.07300 48.67700 scale (grids/A): 2.132886 object centre (A): 1.447001 -1.197499 11.05950 number of atom coordinates read : 2011 total number of charged atoms : 1871 net assigned charge : -0.9999837 assigned positive charge : 302.2589 centred at (gu) : 89.64375 90.26326 89.28390 assigned negative charge : -303.2591 centred at (gu) : 90.11696 90.17364 89.49036 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 72914 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17233 grid for indexing accessible points = 1.400000 m= 28426 mr = 50837 m= 5778 mr = 21890 m= 497 mr = 4003 m= 14 mr = 267 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 765 time to turn everything in is 0.6700000 number of dielectric boundary points 30632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 14870 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) : 0.7109620 object centre at (A) : 1.447001 -1.197499 11.05950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2775300E-03 -6.1578460E-02 midg,1,midg; midg,igrid,midg 1.5337493E-02 -3.0117260E-02 1,midg,midg; igrid,midg,midg 4.5410752E-02 -1.1934364E-02 gauss-seidel spectral radius is 0.9988402 estimated iterations to convergence 232 setup time was (sec) 0.9600000 now iterating at: 07:10:04 rms-change max change #iterations 4.673754 250.4043 at 10iterations 2.302274 79.73432 at 20iterations 1.146955 36.32693 at 30iterations 0.5706272 17.37421 at 40iterations 0.2824436 10.27522 at 50iterations 0.1403518 4.216272 at 60iterations 6.9704302E-02 2.011906 at 70iterations 3.4700379E-02 1.006397 at 80iterations 1.7269809E-02 0.5788994 at 90iterations 8.5964827E-03 0.2770419 at 100iterations 4.2637018E-03 0.1286697 at 110iterations 2.1235456E-03 6.0485840E-02 at 120iterations finished qdiffx linear iterations at : 07:10:13 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 2.1235456E-03 6.0485840E-02 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.380000 DelPhi exited at 07:10:13 9.384u 0.305s 0:09.95 97.2% 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 Sun Oct 9 2011 at 07:10:13 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 3.199329 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): -21.88900 24.78300 ymin,ymax (A): -26.23400 23.83900 zmin,zma (A): -13.27900 35.39800 x,y,z range (A): 46.67200 50.07300 48.67700 scale (grids/A): 3.199329 object centre (A): 1.447001 -1.197499 11.05950 number of atom coordinates read : 2011 total number of charged atoms : 1871 net assigned charge : -0.9999837 assigned positive charge : 302.2589 centred at (gu) : 89.46561 90.39499 88.92581 assigned negative charge : -303.2591 centred at (gu) : 90.17554 90.26040 89.23559 start vw surface at 0.1300000 fill in re-entrant regions at 0.9700000 boundary points on vw surface= 168160 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17233 grid for indexing accessible points = 1.400000 m= 88555 mr = 122397 m= 36516 mr = 74056 m= 10990 mr = 30503 m= 2162 mr = 8829 m= 224 mr = 1600 m= 8 mr = 135 m= 0 mr = 5 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 2321 time to turn everything in is 2.140000 number of dielectric boundary points 69090 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.300000 number of grid points assigned charge 14968 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) : 2.132886 object centre at (A) : 1.447001 -1.197499 11.05950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8457473E-02 -0.6480948 midg,1,midg; midg,igrid,midg 0.2777624 -0.3791337 1,midg,midg; igrid,midg,midg 0.3123878 -0.1160579 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 2.470000 now iterating at: 07:10:16 rms-change max change #iterations 10.22862 458.3218 at 10iterations 5.936176 135.8576 at 20iterations 3.459327 58.34808 at 30iterations 2.015727 36.59973 at 40iterations 1.178862 21.44237 at 50iterations 0.6857551 13.19052 at 60iterations 0.3982535 7.580819 at 70iterations 0.2320924 3.871187 at 80iterations 0.1355087 2.408806 at 90iterations 7.8949839E-02 1.444050 at 100iterations 4.5935214E-02 0.7777290 at 110iterations 2.6766449E-02 0.4649200 at 120iterations 1.5606973E-02 0.2469864 at 130iterations 9.0800449E-03 0.1569922 at 140iterations 5.2907695E-03 0.1007118 at 150iterations 3.0904091E-03 5.3909302E-02 at 160iterations 1.7982367E-03 3.2632351E-02 at 170iterations 1.0460739E-03 1.8135548E-02 at 180iterations finished qdiffx linear iterations at : 07:10:30 total time elapsed so far: 16.20000 # loops : 180 mean,max change (kT/e) : 1.0460739E-03 1.8135548E-02 energy calculations done at 16.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.39000 DelPhi exited at 07:10:30 16.390u 0.299s 0:16.94 98.4% 0+0k 0+0io 0pf+0w