Sun Oct 9 21:08:52 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 21:08:53 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 = 3182 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: 0.6063290 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): 44.16900 98.86400 ymin,ymax (A): 3.089000 61.80300 zmin,zma (A): 14.97200 67.49000 x,y,z range (A): 54.69500 58.71400 52.51800 scale (grids/A): 0.6063290 object centre (A): 71.51650 32.44600 41.23100 number of atom coordinates read : 3182 total number of charged atoms : 3128 net assigned charge : 8.500025 assigned positive charge : 498.1896 centred at (gu) : 90.85963 87.86414 90.48760 assigned negative charge : -489.6910 centred at (gu) : 90.79093 87.75784 90.51160 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8144 nv = 96 ne = 84 npr = 58156 no. pairs analyzed = 58156 no. exposed pairs = 4461 no. arc points = 33133 no. surface atoms = 1481 nbur = 1701 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 3974 m= 4 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3367 ## 326 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10165 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2863927E-09 3.5719123E-09 midg,1,midg; midg,igrid,midg -2.5218505E-09 6.4774359E-09 1,midg,midg; igrid,midg,midg 6.2107436E-10 1.0109579E-08 gauss-seidel spectral radius is 0.9859898 estimated iterations to convergence 69 setup time was (sec) 0.6700000 now iterating at: 21:08:54 rms-change max change #iterations 0.1257172 19.98920 at 10iterations 1.0767436E-02 1.841835 at 20iterations 9.4759325E-04 0.1477729 at 30iterations 8.3471816E-05 1.2417078E-02 at 40iterations 7.3251886E-06 9.7656250E-04 at 50iterations finished qdiffx linear iterations at : 21:08:58 total time elapsed so far: 5.060000 # loops : 50 mean,max change (kT/e) : 7.3251886E-06 9.7656250E-04 energy calculations done at 5.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.230000 DelPhi exited at 21:08:59 5.235u 0.463s 0:05.99 94.9% 0+0k 0+0io 6pf+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 21:08:59 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 = 3182 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: 1.818987 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): 44.16900 98.86400 ymin,ymax (A): 3.089000 61.80300 zmin,zma (A): 14.97200 67.49000 x,y,z range (A): 54.69500 58.71400 52.51800 scale (grids/A): 1.818987 object centre (A): 71.51650 32.44600 41.23100 number of atom coordinates read : 3182 total number of charged atoms : 3128 net assigned charge : 8.500025 assigned positive charge : 498.1896 centred at (gu) : 92.57803 83.59133 91.46207 assigned negative charge : -489.6910 centred at (gu) : 92.37243 83.27299 91.53426 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87495 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33133 grid for indexing accessible points = 1.400000 m= 28975 mr = 56691 m= 4162 mr = 19826 m= 248 mr = 2239 m= 3 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 239 time to turn everything in is 0.7400000 number of dielectric boundary points 42065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 240 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 24409 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) : 0.6063290 object centre at (A) : 71.51650 32.44600 41.23100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8099525E-04 -8.7593133E-03 midg,1,midg; midg,igrid,midg 6.0610071E-02 6.9779932E-02 1,midg,midg; igrid,midg,midg 2.2427919E-03 1.7060451E-02 gauss-seidel spectral radius is 0.9985972 estimated iterations to convergence 212 setup time was (sec) 1.140000 now iterating at: 21:09:00 rms-change max change #iterations 4.390621 173.3300 at 10iterations 2.027309 65.86415 at 20iterations 0.9327343 28.95696 at 30iterations 0.4314849 14.96748 at 40iterations 0.1988439 6.291954 at 50iterations 9.2067435E-02 2.749678 at 60iterations 4.2577952E-02 1.257310 at 70iterations 1.9660220E-02 0.5618286 at 80iterations 9.0966430E-03 0.2617769 at 90iterations 4.2152018E-03 0.1467409 at 100iterations 1.9502473E-03 6.0577393E-02 at 110iterations 9.0205891E-04 2.8716087E-02 at 120iterations finished qdiffx linear iterations at : 21:09:12 total time elapsed so far: 12.91000 # loops : 120 mean,max change (kT/e) : 9.0205891E-04 2.8716087E-02 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 21:09:12 13.087u 0.515s 0:13.88 97.9% 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 21:09:12 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 = 3182 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: 2.728481 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): 44.16900 98.86400 ymin,ymax (A): 3.089000 61.80300 zmin,zma (A): 14.97200 67.49000 x,y,z range (A): 54.69500 58.71400 52.51800 scale (grids/A): 2.728481 object centre (A): 71.51650 32.44600 41.23100 number of atom coordinates read : 3182 total number of charged atoms : 3128 net assigned charge : 8.500025 assigned positive charge : 498.1896 centred at (gu) : 93.86694 80.38681 92.19298 assigned negative charge : -489.6910 centred at (gu) : 93.55865 79.90942 92.30130 start vw surface at 0.1300000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 202196 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33133 grid for indexing accessible points = 1.400000 m= 95681 mr = 138714 m= 31637 mr = 74856 m= 7025 mr = 23766 m= 897 mr = 4830 m= 63 mr = 555 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 872 time to turn everything in is 1.880000 number of dielectric boundary points 94759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 25020 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) : 1.818987 object centre at (A) : 71.51650 32.44600 41.23100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4726633E-02 -0.1990302 midg,1,midg; midg,igrid,midg 0.5548360 0.9726139 1,midg,midg; igrid,midg,midg 7.6534510E-02 0.1520625 gauss-seidel spectral radius is 0.9992790 estimated iterations to convergence 294 setup time was (sec) 2.300000 now iterating at: 21:09:15 rms-change max change #iterations 10.82719 345.8963 at 10iterations 6.530927 154.2339 at 20iterations 3.888213 85.99590 at 30iterations 2.292731 57.39159 at 40iterations 1.346722 27.43667 at 50iterations 0.7910830 16.70424 at 60iterations 0.4620989 10.03690 at 70iterations 0.2701415 4.630242 at 80iterations 0.1572467 3.023468 at 90iterations 9.1403343E-02 1.707209 at 100iterations 5.3216025E-02 0.9716082 at 110iterations 3.0891687E-02 0.5635891 at 120iterations 1.7948883E-02 0.3236098 at 130iterations 1.0403509E-02 0.2004732 at 140iterations 6.0320357E-03 0.1071510 at 150iterations 3.4982767E-03 6.2681198E-02 at 160iterations 2.0280383E-03 3.5095453E-02 at 170iterations 1.1729129E-03 2.3136139E-02 at 180iterations finished qdiffx linear iterations at : 21:09:35 total time elapsed so far: 22.50000 # loops : 180 mean,max change (kT/e) : 1.1729129E-03 2.3136139E-02 energy calculations done at 22.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.68000 DelPhi exited at 21:09:36 22.682u 0.539s 0:23.60 98.3% 0+0k 0+0io 0pf+0w