Sun Oct 9 13:21:52 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 13:21:52 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 = 2402 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: 0.6729933 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): -7.228000 44.36000 ymin,ymax (A): -14.29100 38.60700 zmin,zma (A): 1.434000 44.76600 x,y,z range (A): 51.58800 52.89800 43.33200 scale (grids/A): 0.6729933 object centre (A): 18.56600 12.15800 23.10000 number of atom coordinates read : 2402 total number of charged atoms : 2260 net assigned charge : 3.500024 assigned positive charge : 366.4560 centred at (gu) : 89.87141 90.79298 90.83060 assigned negative charge : -362.9565 centred at (gu) : 89.85538 90.97025 90.89917 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7324 nv = 96 ne = 84 npr = 48338 no. pairs analyzed = 48338 no. exposed pairs = 3016 no. arc points = 20951 no. surface atoms = 1016 nbur = 1386 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4048 m= 2 mr = 65 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 3646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2066 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8511 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5864262E-08 -5.5224945E-09 midg,1,midg; midg,igrid,midg 4.9081098E-08 -3.9216214E-08 1,midg,midg; igrid,midg,midg 9.2904529E-09 1.6832141E-08 gauss-seidel spectral radius is 0.9885346 estimated iterations to convergence 76 setup time was (sec) 0.5400000 now iterating at: 13:21:53 rms-change max change #iterations 0.1705466 25.06128 at 10iterations 1.9664720E-02 3.015665 at 20iterations 2.7629784E-03 0.3901672 at 30iterations 7.1026682E-04 0.1024971 at 40iterations 2.5390892E-04 3.6643982E-02 at 50iterations finished qdiffx linear iterations at : 13:21:56 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 2.5390892E-04 3.6643982E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 13:21:56 3.384u 0.143s 0:03.83 91.9% 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 13:21:56 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 = 2402 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: 2.018980 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): -7.228000 44.36000 ymin,ymax (A): -14.29100 38.60700 zmin,zma (A): 1.434000 44.76600 x,y,z range (A): 51.58800 52.89800 43.33200 scale (grids/A): 2.018980 object centre (A): 18.56600 12.15800 23.10000 number of atom coordinates read : 2402 total number of charged atoms : 2260 net assigned charge : 3.500024 assigned positive charge : 366.4560 centred at (gu) : 89.61364 92.37843 92.49151 assigned negative charge : -362.9565 centred at (gu) : 89.56580 92.91028 92.69730 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20951 grid for indexing accessible points = 1.400000 m= 29528 mr = 53702 m= 5182 mr = 21816 m= 403 mr = 3280 m= 7 mr = 201 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 118 time to turn everything in is 0.5900000 number of dielectric boundary points 33642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 17886 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) : 0.6729933 object centre at (A) : 18.56600 12.15800 23.10000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7717905E-02 9.9023329E-03 midg,1,midg; midg,igrid,midg 1.5932167E-02 -5.4491241E-02 1,midg,midg; igrid,midg,midg 3.7342157E-02 9.5434617E-03 gauss-seidel spectral radius is 0.9987610 estimated iterations to convergence 225 setup time was (sec) 0.8800000 now iterating at: 13:21:57 rms-change max change #iterations 4.569603 183.7692 at 10iterations 2.212838 69.02667 at 20iterations 1.078542 35.94678 at 30iterations 0.5245513 16.73486 at 40iterations 0.2542808 7.514534 at 50iterations 0.1235612 3.751704 at 60iterations 6.0471952E-02 1.919501 at 70iterations 2.9468089E-02 0.8343430 at 80iterations 1.4572509E-02 0.4544296 at 90iterations 7.3319376E-03 0.2206287 at 100iterations 3.8053512E-03 0.1209288 at 110iterations 2.0850683E-03 6.2707901E-02 at 120iterations finished qdiffx linear iterations at : 13:22:04 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 2.0850683E-03 6.2707901E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 13:22:05 7.701u 0.184s 0:08.20 96.0% 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 13:22:05 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 = 2402 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: 3.028470 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): -7.228000 44.36000 ymin,ymax (A): -14.29100 38.60700 zmin,zma (A): 1.434000 44.76600 x,y,z range (A): 51.58800 52.89800 43.33200 scale (grids/A): 3.028470 object centre (A): 18.56600 12.15800 23.10000 number of atom coordinates read : 2402 total number of charged atoms : 2260 net assigned charge : 3.500024 assigned positive charge : 366.4560 centred at (gu) : 89.42049 93.56760 93.73708 assigned negative charge : -362.9565 centred at (gu) : 89.34863 94.36543 94.04589 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 178763 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20951 grid for indexing accessible points = 1.400000 m= 93334 mr = 129873 m= 35944 mr = 76366 m= 9655 mr = 28980 m= 1758 mr = 7277 m= 161 mr = 1232 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 414 time to turn everything in is 1.540000 number of dielectric boundary points 75789 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 18076 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) : 2.018980 object centre at (A) : 18.56600 12.15800 23.10000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3960377 6.7277001E-03 midg,1,midg; midg,igrid,midg 0.3296401 -0.6025664 1,midg,midg; igrid,midg,midg 0.4337012 -0.1470197 gauss-seidel spectral radius is 0.9992824 estimated iterations to convergence 295 setup time was (sec) 1.850000 now iterating at: 13:22:07 rms-change max change #iterations 10.48628 403.9238 at 10iterations 6.189860 120.7508 at 20iterations 3.649415 76.01630 at 30iterations 2.143638 42.32449 at 40iterations 1.259157 24.91847 at 50iterations 0.7350950 12.72078 at 60iterations 0.4306630 7.545988 at 70iterations 0.2514246 4.809967 at 80iterations 0.1462447 2.815147 at 90iterations 8.5427873E-02 1.505649 at 100iterations 4.9992412E-02 0.8804016 at 110iterations 2.9318688E-02 0.5108703 at 120iterations 1.7366791E-02 0.3147507 at 130iterations 1.0496820E-02 0.2097588 at 140iterations 6.5459497E-03 0.1252708 at 150iterations 4.2901146E-03 8.5322380E-02 at 160iterations 3.0085640E-03 6.1504364E-02 at 170iterations 2.2446979E-03 4.5852661E-02 at 180iterations finished qdiffx linear iterations at : 13:22:17 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 2.2446979E-03 4.5852661E-02 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 13:22:18 12.473u 0.192s 0:12.92 97.9% 0+0k 0+0io 0pf+0w