Mon Oct 10 17:01:29 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 Mon Oct 10 2011 at 17:01:29 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4139 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5153445 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): -15.19200 36.65800 ymin,ymax (A): -30.61300 31.39800 zmin,zma (A): -4.001000 65.07900 x,y,z range (A): 51.85000 62.01100 69.08000 scale (grids/A): 0.5153445 object centre (A): 10.73300 0.3924990 30.53900 number of atom coordinates read : 4139 total number of charged atoms : 3893 net assigned charge : 5.206021 assigned positive charge : 614.7018 centred at (gu) : 90.19553 90.54982 87.08875 assigned negative charge : -609.4991 centred at (gu) : 90.06008 90.60960 87.08025 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6926 nv = 96 ne = 84 npr = 84375 no. pairs analyzed = 84375 no. exposed pairs = 5329 no. arc points = 37296 no. surface atoms = 1766 nbur = 2373 mkacc time = 0.1900000 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 = 1.652000 m= 242 mr = 3528 m= 0 mr = 9 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3503 ## 531 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 9182 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4359219E-10 5.4781877E-11 midg,1,midg; midg,igrid,midg 2.1657798E-10 -8.1532205E-11 1,midg,midg; igrid,midg,midg -2.6327332E-10 4.7066495E-10 gauss-seidel spectral radius is 0.9806966 estimated iterations to convergence 59 setup time was (sec) 0.6700000 now iterating at: 17:01:30 rms-change max change #iterations 6.6952705E-02 13.21799 at 10iterations 3.9487369E-03 0.6859055 at 20iterations 3.7913123E-04 5.9753418E-02 at 30iterations 1.0350870E-04 1.4313459E-02 at 40iterations 3.5067900E-05 5.3372383E-03 at 50iterations finished qdiffx linear iterations at : 17:01:34 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 3.5067900E-05 5.3372383E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 17:01:34 4.277u 0.222s 0:05.03 89.2% 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 Mon Oct 10 2011 at 17:01:35 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4139 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.546034 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): -15.19200 36.65800 ymin,ymax (A): -30.61300 31.39800 zmin,zma (A): -4.001000 65.07900 x,y,z range (A): 51.85000 62.01100 69.08000 scale (grids/A): 1.546034 object centre (A): 10.73300 0.3924990 30.53900 number of atom coordinates read : 4139 total number of charged atoms : 3893 net assigned charge : 5.206021 assigned positive charge : 614.7018 centred at (gu) : 90.58530 91.64822 81.26484 assigned negative charge : -609.4991 centred at (gu) : 90.18013 91.82840 81.24058 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 77824 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37296 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22379 mr = 52485 m= 2044 mr = 14793 m= 45 mr = 930 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.5800000 number of dielectric boundary points 34084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 488 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 29347 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) : 0.5153445 object centre at (A) : 10.73300 0.3924990 30.53900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1315508E-03 1.0528815E-02 midg,1,midg; midg,igrid,midg -4.8908830E-04 -1.0842979E-02 1,midg,midg; igrid,midg,midg -2.3526801E-03 1.1431623E-02 gauss-seidel spectral radius is 0.9980892 estimated iterations to convergence 182 setup time was (sec) 0.8900000 now iterating at: 17:01:36 rms-change max change #iterations 3.519803 179.6706 at 10iterations 1.424345 53.33977 at 20iterations 0.5826215 19.46365 at 30iterations 0.2364030 8.781218 at 40iterations 9.6682556E-02 3.526054 at 50iterations 3.9399561E-02 1.249531 at 60iterations 1.6063144E-02 0.5609818 at 70iterations 6.5777083E-03 0.2115712 at 80iterations 2.7036120E-03 9.9021912E-02 at 90iterations 1.1181954E-03 3.8091660E-02 at 100iterations 4.7054375E-04 1.7800808E-02 at 110iterations 2.0757710E-04 7.4348450E-03 at 120iterations finished qdiffx linear iterations at : 17:01:44 total time elapsed so far: 9.320000 # loops : 120 mean,max change (kT/e) : 2.0757710E-04 7.4348450E-03 energy calculations done at 9.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.500000 DelPhi exited at 17:01:45 9.505u 0.274s 0:10.36 94.3% 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 17:01:45 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4139 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.319050 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): -15.19200 36.65800 ymin,ymax (A): -30.61300 31.39800 zmin,zma (A): -4.001000 65.07900 x,y,z range (A): 51.85000 62.01100 69.08000 scale (grids/A): 2.319050 object centre (A): 10.73300 0.3924990 30.53900 number of atom coordinates read : 4139 total number of charged atoms : 3893 net assigned charge : 5.206021 assigned positive charge : 614.7018 centred at (gu) : 90.87769 92.47207 76.89689 assigned negative charge : -609.4991 centred at (gu) : 90.26998 92.74268 76.86090 start vw surface at 0.1900000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 181232 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37296 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 80110 mr = 129136 m= 20620 mr = 62276 m= 3077 mr = 14788 m= 152 mr = 1936 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 1.430000 number of dielectric boundary points 76999 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 31072 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) : 1.546034 object centre at (A) : 10.73300 0.3924990 30.53900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1669380 0.2866160 midg,1,midg; midg,igrid,midg -9.7022004E-02 -0.2399867 1,midg,midg; igrid,midg,midg -3.3625931E-02 0.1687443 gauss-seidel spectral radius is 0.9991416 estimated iterations to convergence 270 setup time was (sec) 1.770000 now iterating at: 17:01:47 rms-change max change #iterations 9.517685 303.4469 at 10iterations 5.421406 148.6093 at 20iterations 3.054772 74.15966 at 30iterations 1.717690 39.94781 at 40iterations 0.9620489 24.87193 at 50iterations 0.5358665 12.66921 at 60iterations 0.2984779 7.323437 at 70iterations 0.1656552 3.721685 at 80iterations 9.1817155E-02 2.042746 at 90iterations 5.0926328E-02 1.082407 at 100iterations 2.8102823E-02 0.6986961 at 110iterations 1.5525260E-02 0.3218196 at 120iterations 8.6102076E-03 0.1768951 at 130iterations 4.7494490E-03 9.3271971E-02 at 140iterations 2.6174872E-03 4.9102783E-02 at 150iterations 1.4453218E-03 2.8764725E-02 at 160iterations 7.9786067E-04 1.5010834E-02 at 170iterations 4.4039966E-04 9.6154213E-03 at 180iterations finished qdiffx linear iterations at : 17:02:01 total time elapsed so far: 15.36000 # loops : 180 mean,max change (kT/e) : 4.4039966E-04 9.6154213E-03 energy calculations done at 15.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.54000 DelPhi exited at 17:02:02 15.537u 0.265s 0:17.28 91.3% 0+0k 0+0io 0pf+0w