Tue Oct 11 06:45:50 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 Tue Oct 11 2011 at 06:45:50 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 = 3456 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5745457 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): 7.683000 64.74700 ymin,ymax (A): -19.17700 42.78500 zmin,zma (A): 37.29300 87.47800 x,y,z range (A): 57.06400 61.96200 50.18501 scale (grids/A): 0.5745457 object centre (A): 36.21500 11.80400 62.38550 number of atom coordinates read : 3456 total number of charged atoms : 3377 net assigned charge : -8.999975 assigned positive charge : 527.9775 centred at (gu) : 92.63625 90.32056 90.32196 assigned negative charge : -536.9786 centred at (gu) : 92.58289 90.07108 90.17477 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7714 nv = 96 ne = 84 npr = 66790 no. pairs analyzed = 66790 no. exposed pairs = 4655 no. arc points = 32780 no. surface atoms = 1565 nbur = 1891 mkacc time = 0.1500000 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 = 1.484000 m= 332 mr = 3876 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3267 ## 326 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9820 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5958259E-09 1.6411389E-09 midg,1,midg; midg,igrid,midg -6.7807666E-09 3.9561385E-09 1,midg,midg; igrid,midg,midg -1.5515601E-09 -8.5726293E-10 gauss-seidel spectral radius is 0.9844154 estimated iterations to convergence 66 setup time was (sec) 0.6200000 now iterating at: 06:45:50 rms-change max change #iterations 0.1046465 18.43340 at 10iterations 7.9822587E-03 1.237686 at 20iterations 8.5839920E-04 0.1511812 at 30iterations 2.0756792E-04 3.9709568E-02 at 40iterations 6.8793110E-05 1.4657974E-02 at 50iterations finished qdiffx linear iterations at : 06:45:53 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 6.8793110E-05 1.4657974E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 06:45:54 3.459u 0.173s 0:04.31 83.9% 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 Tue Oct 11 2011 at 06:45:54 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 = 3456 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.723637 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): 7.683000 64.74700 ymin,ymax (A): -19.17700 42.78500 zmin,zma (A): 37.29300 87.47800 x,y,z range (A): 57.06400 61.96200 50.18501 scale (grids/A): 1.723637 object centre (A): 36.21500 11.80400 62.38550 number of atom coordinates read : 3456 total number of charged atoms : 3377 net assigned charge : -8.999975 assigned positive charge : 527.9775 centred at (gu) : 97.90784 90.96088 90.96521 assigned negative charge : -536.9786 centred at (gu) : 97.74822 90.21275 90.52436 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32780 grid for indexing accessible points = 1.400000 m= 26624 mr = 56389 m= 2951 mr = 17836 m= 108 mr = 1361 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 38477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 256 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 26150 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) : 0.5745457 object centre at (A) : 36.21500 11.80400 62.38550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3619283E-02 1.2883602E-02 midg,1,midg; midg,igrid,midg -2.5459528E-02 3.8410045E-02 1,midg,midg; igrid,midg,midg -1.6318571E-02 -1.0624093E-02 gauss-seidel spectral radius is 0.9984348 estimated iterations to convergence 201 setup time was (sec) 0.8600000 now iterating at: 06:45:55 rms-change max change #iterations 4.154609 169.0488 at 10iterations 1.838172 67.98945 at 20iterations 0.8107951 27.35217 at 30iterations 0.3589616 11.95276 at 40iterations 0.1603375 5.444986 at 50iterations 7.1152180E-02 2.198040 at 60iterations 3.1535346E-02 0.9880085 at 70iterations 1.4078481E-02 0.4839792 at 80iterations 6.2972610E-03 0.1925201 at 90iterations 2.8426640E-03 9.0225220E-02 at 100iterations 1.3043071E-03 4.2182922E-02 at 110iterations 6.2215823E-04 2.1138992E-02 at 120iterations finished qdiffx linear iterations at : 06:46:02 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 6.2215823E-04 2.1138992E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 06:46:02 7.521u 0.234s 0:08.28 93.5% 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 06:46:02 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 = 3456 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: 2.585456 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): 7.683000 64.74700 ymin,ymax (A): -19.17700 42.78500 zmin,zma (A): 37.29300 87.47800 x,y,z range (A): 57.06400 61.96200 50.18501 scale (grids/A): 2.585456 object centre (A): 36.21500 11.80400 62.38550 number of atom coordinates read : 3456 total number of charged atoms : 3377 net assigned charge : -8.999975 assigned positive charge : 527.9775 centred at (gu) : 101.8615 91.44102 91.44743 assigned negative charge : -536.9786 centred at (gu) : 101.6224 90.31906 90.78638 start vw surface at 0.1800000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 195702 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32780 grid for indexing accessible points = 1.400000 m= 91523 mr = 138192 m= 26661 mr = 71501 m= 4750 mr = 19401 m= 417 mr = 2989 m= 12 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.400000 number of dielectric boundary points 86816 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 27000 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) : 1.723637 object centre at (A) : 36.21500 11.80400 62.38550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1862323 0.1828091 midg,1,midg; midg,igrid,midg -0.1107973 0.5648258 1,midg,midg; igrid,midg,midg -0.1935699 -9.2697270E-02 gauss-seidel spectral radius is 0.9992349 estimated iterations to convergence 285 setup time was (sec) 1.700000 now iterating at: 06:46:04 rms-change max change #iterations 10.50259 311.4163 at 10iterations 6.202955 152.0981 at 20iterations 3.625462 77.54623 at 30iterations 2.108318 43.95390 at 40iterations 1.224365 23.81397 at 50iterations 0.7040697 14.12698 at 60iterations 0.4051617 7.874937 at 70iterations 0.2334204 4.602032 at 80iterations 0.1338270 2.653181 at 90iterations 7.6651514E-02 1.619008 at 100iterations 4.3812782E-02 0.9095573 at 110iterations 2.5062796E-02 0.4559021 at 120iterations 1.4338109E-02 0.2586670 at 130iterations 8.2121678E-03 0.1630640 at 140iterations 4.7213282E-03 0.1020861 at 150iterations 2.7187858E-03 5.4431915E-02 at 160iterations 1.5842906E-03 3.0792236E-02 at 170iterations 9.3602471E-04 2.0008087E-02 at 180iterations finished qdiffx linear iterations at : 06:46:14 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 9.3602471E-04 2.0008087E-02 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.11000 DelPhi exited at 06:46:15 12.114u 0.208s 0:12.67 97.1% 0+0k 0+0io 0pf+0w