Sat Oct 8 17:28:15 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 Sat Oct 8 2011 at 17:28:15 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 = 3576 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: 0.5377806 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): -2.127000 64.07100 ymin,ymax (A): 14.23300 76.43300 zmin,zma (A): -13.24800 34.34000 x,y,z range (A): 66.19800 62.20000 47.58800 scale (grids/A): 0.5377806 object centre (A): 30.97200 45.33300 10.54600 number of atom coordinates read : 3576 total number of charged atoms : 3429 net assigned charge : -6.999992 assigned positive charge : 540.7421 centred at (gu) : 89.42425 87.39232 89.66927 assigned negative charge : -547.7438 centred at (gu) : 89.40267 87.41467 89.70160 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6620 nv = 96 ne = 84 npr = 72701 no. pairs analyzed = 72701 no. exposed pairs = 4336 no. arc points = 30253 no. surface atoms = 1456 nbur = 2120 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 = 1.568000 m= 246 mr = 3552 m= 0 mr = 13 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2996 ## 401 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8724 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3393149E-10 -4.6859472E-10 midg,1,midg; midg,igrid,midg -3.4127831E-10 -2.3797131E-10 1,midg,midg; igrid,midg,midg -5.1236621E-10 -1.6400180E-10 gauss-seidel spectral radius is 0.9822185 estimated iterations to convergence 62 setup time was (sec) 0.6400000 now iterating at: 17:28:16 rms-change max change #iterations 7.2967552E-02 12.03089 at 10iterations 4.8526358E-03 0.7944069 at 20iterations 3.4692409E-04 5.8368683E-02 at 30iterations 4.7129019E-05 8.9473724E-03 at 40iterations 1.0737331E-05 2.4361610E-03 at 50iterations finished qdiffx linear iterations at : 17:28:20 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 1.0737331E-05 2.4361610E-03 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 17:28:20 4.611u 0.387s 0:05.26 94.8% 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 Sat Oct 8 2011 at 17:28:20 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 = 3576 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: 1.613342 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): -2.127000 64.07100 ymin,ymax (A): 14.23300 76.43300 zmin,zma (A): -13.24800 34.34000 x,y,z range (A): 66.19800 62.20000 47.58800 scale (grids/A): 1.613342 object centre (A): 30.97200 45.33300 10.54600 number of atom coordinates read : 3576 total number of charged atoms : 3429 net assigned charge : -6.999992 assigned positive charge : 540.7421 centred at (gu) : 88.27203 82.17630 89.00711 assigned negative charge : -547.7438 centred at (gu) : 88.20740 82.24359 89.10455 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 74456 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30253 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22695 mr = 52075 m= 2309 mr = 15727 m= 54 mr = 1147 m= 0 mr = 3 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1865 time to turn everything in is 0.6100000 number of dielectric boundary points 30562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 334 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 26180 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) : 0.5377806 object centre at (A) : 30.97200 45.33300 10.54600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3541516E-03 -1.8720975E-03 midg,1,midg; midg,igrid,midg -2.1915499E-02 -1.5293305E-02 1,midg,midg; igrid,midg,midg 1.1553671E-02 -5.3853919E-03 gauss-seidel spectral radius is 0.9981863 estimated iterations to convergence 187 setup time was (sec) 0.9100000 now iterating at: 17:28:22 rms-change max change #iterations 3.603854 176.2359 at 10iterations 1.503550 56.05213 at 20iterations 0.6257064 21.97167 at 30iterations 0.2619714 8.853091 at 40iterations 0.1094024 3.422194 at 50iterations 4.5713101E-02 1.596279 at 60iterations 1.9080082E-02 0.6516685 at 70iterations 7.9927081E-03 0.2790871 at 80iterations 3.3513485E-03 0.1072822 at 90iterations 1.4041133E-03 4.8673630E-02 at 100iterations 5.8936048E-04 2.1699905E-02 at 110iterations 2.4961954E-04 8.1284046E-03 at 120iterations finished qdiffx linear iterations at : 17:28:31 total time elapsed so far: 10.45000 # loops : 120 mean,max change (kT/e) : 2.4961954E-04 8.1284046E-03 energy calculations done at 10.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.62000 DelPhi exited at 17:28:32 10.624u 0.440s 0:11.36 97.3% 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 Sat Oct 8 2011 at 17:28:32 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 = 3576 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: 2.420013 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): -2.127000 64.07100 ymin,ymax (A): 14.23300 76.43300 zmin,zma (A): -13.24800 34.34000 x,y,z range (A): 66.19800 62.20000 47.58800 scale (grids/A): 2.420013 object centre (A): 30.97200 45.33300 10.54600 number of atom coordinates read : 3576 total number of charged atoms : 3429 net assigned charge : -6.999992 assigned positive charge : 540.7421 centred at (gu) : 87.40788 78.26416 88.51048 assigned negative charge : -547.7438 centred at (gu) : 87.31118 78.36522 88.65678 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 172926 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30253 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 79729 mr = 126850 m= 22388 mr = 63600 m= 3661 mr = 16901 m= 259 mr = 2479 m= 2 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 6485 time to turn everything in is 1.500000 number of dielectric boundary points 69037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 27386 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) : 1.613342 object centre at (A) : 30.97200 45.33300 10.54600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4167108E-02 -1.4912837E-02 midg,1,midg; midg,igrid,midg -0.4539954 -0.2778439 1,midg,midg; igrid,midg,midg 0.4203692 -7.6889165E-02 gauss-seidel spectral radius is 0.9991428 estimated iterations to convergence 270 setup time was (sec) 1.860000 now iterating at: 17:28:34 rms-change max change #iterations 9.332708 301.0585 at 10iterations 5.218900 120.8443 at 20iterations 2.908994 69.16177 at 30iterations 1.615822 34.62678 at 40iterations 0.8940226 18.69307 at 50iterations 0.4955154 10.76145 at 60iterations 0.2746648 5.315176 at 70iterations 0.1515799 3.059937 at 80iterations 8.3544016E-02 1.620749 at 90iterations 4.6083752E-02 0.8545761 at 100iterations 2.5428096E-02 0.4765291 at 110iterations 1.4023189E-02 0.2761889 at 120iterations 7.7355849E-03 0.1527138 at 130iterations 4.2715762E-03 8.2462311E-02 at 140iterations 2.3518333E-03 4.3655396E-02 at 150iterations 1.2992310E-03 2.6526809E-02 at 160iterations 7.2053366E-04 1.4173508E-02 at 170iterations 4.0201846E-04 7.7943802E-03 at 180iterations finished qdiffx linear iterations at : 17:28:50 total time elapsed so far: 17.82000 # loops : 180 mean,max change (kT/e) : 4.0201846E-04 7.7943802E-03 energy calculations done at 17.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.99000 DelPhi exited at 17:28:50 17.998u 0.452s 0:18.72 98.5% 0+0k 0+0io 0pf+0w