Tue Oct 11 04:19:27 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 04:19:27 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2695 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: 0.6827379 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): -14.78200 33.27000 ymin,ymax (A): 7.424000 55.58000 zmin,zma (A): 25.73700 77.88000 x,y,z range (A): 48.05200 48.15600 52.14300 scale (grids/A): 0.6827379 object centre (A): 9.244000 31.50200 51.80850 number of atom coordinates read : 2695 total number of charged atoms : 2548 net assigned charge : 3.500014 assigned positive charge : 410.9499 centred at (gu) : 89.97934 90.51305 88.95901 assigned negative charge : -407.4503 centred at (gu) : 90.23191 90.33524 88.97581 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8449 nv = 96 ne = 84 npr = 55497 no. pairs analyzed = 55497 no. exposed pairs = 3259 no. arc points = 22573 no. surface atoms = 1092 nbur = 1603 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 521 mr = 4895 m= 3 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.3100000 number of dielectric boundary points 3991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2073 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9701 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7007470E-08 8.0032292E-09 midg,1,midg; midg,igrid,midg -4.5064652E-08 8.8274213E-08 1,midg,midg; igrid,midg,midg 1.0601337E-07 -7.8334281E-08 gauss-seidel spectral radius is 0.9888824 estimated iterations to convergence 77 setup time was (sec) 0.5100000 now iterating at: 04:19:27 rms-change max change #iterations 0.2015102 27.42986 at 10iterations 2.3081955E-02 2.948784 at 20iterations 2.7220803E-03 0.3277912 at 30iterations 3.3757888E-04 4.9552917E-02 at 40iterations 4.9293398E-05 6.9808960E-03 at 50iterations finished qdiffx linear iterations at : 04:19:30 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 4.9293398E-05 6.9808960E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 04:19:31 3.113u 0.157s 0:03.87 84.2% 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 04:19:31 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2695 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: 2.048214 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): -14.78200 33.27000 ymin,ymax (A): 7.424000 55.58000 zmin,zma (A): 25.73700 77.88000 x,y,z range (A): 48.05200 48.15600 52.14300 scale (grids/A): 2.048214 object centre (A): 9.244000 31.50200 51.80850 number of atom coordinates read : 2695 total number of charged atoms : 2548 net assigned charge : 3.500014 assigned positive charge : 410.9499 centred at (gu) : 89.93767 91.53870 86.87637 assigned negative charge : -407.4503 centred at (gu) : 90.69553 91.00540 86.92697 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 90555 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22573 grid for indexing accessible points = 1.400000 m= 35019 mr = 64786 m= 6128 mr = 26591 m= 468 mr = 3979 m= 13 mr = 209 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1168 time to turn everything in is 0.6100000 number of dielectric boundary points 36618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 20200 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) : 0.6827379 object centre at (A) : 9.244000 31.50200 51.80850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3538203E-02 8.5464315E-03 midg,1,midg; midg,igrid,midg -1.9162532E-02 4.2144738E-02 1,midg,midg; igrid,midg,midg 9.5719419E-02 -1.7890655E-02 gauss-seidel spectral radius is 0.9988185 estimated iterations to convergence 230 setup time was (sec) 0.8700000 now iterating at: 04:19:32 rms-change max change #iterations 5.055428 234.1125 at 10iterations 2.494179 88.75581 at 20iterations 1.234951 35.72335 at 30iterations 0.6112186 16.46949 at 40iterations 0.3027385 8.656861 at 50iterations 0.1495328 4.288603 at 60iterations 7.4171901E-02 2.159872 at 70iterations 3.6701906E-02 1.002941 at 80iterations 1.8174220E-02 0.5307751 at 90iterations 8.9965854E-03 0.2632518 at 100iterations 4.4607082E-03 0.1262054 at 110iterations 2.2235718E-03 6.3347816E-02 at 120iterations finished qdiffx linear iterations at : 04:19:38 total time elapsed so far: 6.950000 # loops : 120 mean,max change (kT/e) : 2.2235718E-03 6.3347816E-02 energy calculations done at 6.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.120000 DelPhi exited at 04:19:38 7.127u 0.171s 0:07.66 95.1% 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 04:19:38 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2695 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: 3.072320 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): -14.78200 33.27000 ymin,ymax (A): 7.424000 55.58000 zmin,zma (A): 25.73700 77.88000 x,y,z range (A): 48.05200 48.15600 52.14300 scale (grids/A): 3.072320 object centre (A): 9.244000 31.50200 51.80850 number of atom coordinates read : 2695 total number of charged atoms : 2548 net assigned charge : 3.500014 assigned positive charge : 410.9499 centred at (gu) : 89.90633 92.30816 85.31469 assigned negative charge : -407.4503 centred at (gu) : 91.04302 91.50816 85.39053 start vw surface at 0.1500000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 209179 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22573 grid for indexing accessible points = 1.400000 m= 111427 mr = 155956 m= 42969 mr = 93088 m= 11303 mr = 35310 m= 1994 mr = 8659 m= 178 mr = 1387 m= 6 mr = 89 m= 0 mr = 4 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 3787 time to turn everything in is 1.600000 number of dielectric boundary points 82563 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 20384 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) : 2.048214 object centre at (A) : 9.244000 31.50200 51.80850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3526198 1.5737051E-02 midg,1,midg; midg,igrid,midg -0.1682378 0.4895783 1,midg,midg; igrid,midg,midg 0.7509335 -0.1049070 gauss-seidel spectral radius is 0.9993001 estimated iterations to convergence 298 setup time was (sec) 1.870000 now iterating at: 04:19:40 rms-change max change #iterations 11.31115 481.9789 at 10iterations 6.648289 130.5362 at 20iterations 3.916940 72.05025 at 30iterations 2.300553 39.06625 at 40iterations 1.349035 21.89219 at 50iterations 0.7921416 13.85569 at 60iterations 0.4643628 8.030359 at 70iterations 0.2721988 4.507211 at 80iterations 0.1594347 2.668027 at 90iterations 9.3287028E-02 1.438331 at 100iterations 5.4688435E-02 0.8598862 at 110iterations 3.2056972E-02 0.5618315 at 120iterations 1.8759487E-02 0.2985840 at 130iterations 1.1021933E-02 0.1882668 at 140iterations 6.4974162E-03 0.1054153 at 150iterations 3.8681994E-03 6.5002441E-02 at 160iterations 2.3253926E-03 4.3426514E-02 at 170iterations 1.4283878E-03 2.5308609E-02 at 180iterations finished qdiffx linear iterations at : 04:19:50 total time elapsed so far: 11.37000 # loops : 180 mean,max change (kT/e) : 1.4283878E-03 2.5308609E-02 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 04:19:51 11.564u 0.184s 0:12.41 94.6% 0+0k 0+0io 0pf+0w