Sat Oct 15 13:24:53 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 15 2011 at 13:24:53 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5907929 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): -35.28200 10.11700 ymin,ymax (A): 1.296000 41.66000 zmin,zma (A): -1.630000 58.62800 x,y,z range (A): 45.39900 40.36400 60.25800 scale (grids/A): 0.5907929 object centre (A): -12.58250 21.47800 28.49900 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.35867 89.45823 89.55756 assigned negative charge : -284.8263 centred at (gu) : 90.30493 89.60015 89.54263 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4636 nv = 96 ne = 84 npr = 40115 no. pairs analyzed = 40115 no. exposed pairs = 2433 no. arc points = 16894 no. surface atoms = 831 nbur = 1133 mkacc time = 8.0000006E-02 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= 198 mr = 2501 m= 0 mr = 22 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1725 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5639 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9397160E-10 1.1127048E-09 midg,1,midg; midg,igrid,midg 4.2288542E-09 -1.7241074E-09 1,midg,midg; igrid,midg,midg -1.3806298E-10 2.1726305E-09 gauss-seidel spectral radius is 0.9851228 estimated iterations to convergence 67 setup time was (sec) 0.4400000 now iterating at: 13:24:53 rms-change max change #iterations 8.4183641E-02 15.11915 at 10iterations 6.8762274E-03 1.156929 at 20iterations 5.5279350E-04 9.5737457E-02 at 30iterations 4.5170105E-05 7.5836182E-03 at 40iterations 3.7177465E-06 5.9890747E-04 at 50iterations finished qdiffx linear iterations at : 13:24:56 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 3.7177465E-06 5.9890747E-04 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 13:24:56 3.151u 0.189s 0:03.64 91.4% 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 15 2011 at 13:24:56 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.772379 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): -35.28200 10.11700 ymin,ymax (A): 1.296000 41.66000 zmin,zma (A): -1.630000 58.62800 x,y,z range (A): 45.39900 40.36400 60.25800 scale (grids/A): 1.772379 object centre (A): -12.58250 21.47800 28.49900 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.07578 88.37463 88.67272 assigned negative charge : -284.8263 centred at (gu) : 90.91490 88.80065 88.62810 start vw surface at 0.1400000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 49994 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16894 grid for indexing accessible points = 1.400000 m= 17783 mr = 34258 m= 2402 mr = 13347 m= 111 mr = 1487 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 338 time to turn everything in is 0.4000000 number of dielectric boundary points 21176 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 14278 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) : 0.5907929 object centre at (A) : -12.58250 21.47800 28.49900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9556880E-02 2.0353468E-02 midg,1,midg; midg,igrid,midg 3.2565522E-03 -6.2774722E-03 1,midg,midg; igrid,midg,midg -1.2076455E-03 -1.7073206E-03 gauss-seidel spectral radius is 0.9983481 estimated iterations to convergence 195 setup time was (sec) 0.6800000 now iterating at: 13:24:57 rms-change max change #iterations 3.090966 156.9323 at 10iterations 1.331203 56.74142 at 20iterations 0.5816179 23.43926 at 30iterations 0.2520742 9.789733 at 40iterations 0.1087055 4.203062 at 50iterations 4.7273964E-02 1.811649 at 60iterations 2.0524796E-02 0.7900887 at 70iterations 8.9211315E-03 0.3384504 at 80iterations 3.8681871E-03 0.1505737 at 90iterations 1.6896077E-03 7.0639819E-02 at 100iterations 7.3080347E-04 2.6615143E-02 at 110iterations 3.1779430E-04 1.3065338E-02 at 120iterations finished qdiffx linear iterations at : 13:25:04 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 3.1779430E-04 1.3065338E-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 13:25:04 7.521u 0.194s 0:08.08 95.4% 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 15 2011 at 13:25:05 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.658568 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): -35.28200 10.11700 ymin,ymax (A): 1.296000 41.66000 zmin,zma (A): -1.630000 58.62800 x,y,z range (A): 45.39900 40.36400 60.25800 scale (grids/A): 2.658568 object centre (A): -12.58250 21.47800 28.49900 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.61378 87.56187 88.00914 assigned negative charge : -284.8263 centred at (gu) : 91.37244 88.20107 87.94211 start vw surface at 0.1300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 115407 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16894 grid for indexing accessible points = 1.400000 m= 58225 mr = 82865 m= 20398 mr = 48087 m= 4122 mr = 16652 m= 463 mr = 3046 m= 17 mr = 279 m= 0 mr = 3 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 1153 time to turn everything in is 0.9000000 number of dielectric boundary points 47700 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 14644 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) : 1.772379 object centre at (A) : -12.58250 21.47800 28.49900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1012881 0.1467714 midg,1,midg; midg,igrid,midg -2.4433956E-03 -9.7797513E-02 1,midg,midg; igrid,midg,midg -3.7895776E-02 -4.6425179E-02 gauss-seidel spectral radius is 0.9991556 estimated iterations to convergence 272 setup time was (sec) 1.180000 now iterating at: 13:25:06 rms-change max change #iterations 7.538033 317.4470 at 10iterations 4.235646 128.3001 at 20iterations 2.378241 62.41042 at 30iterations 1.322625 40.29167 at 40iterations 0.7337728 18.85235 at 50iterations 0.4066273 9.905613 at 60iterations 0.2252473 5.369782 at 70iterations 0.1248870 2.882343 at 80iterations 6.8614058E-02 1.618040 at 90iterations 3.8008168E-02 0.7921181 at 100iterations 2.1051433E-02 0.4996796 at 110iterations 1.1654753E-02 0.2730675 at 120iterations 6.4392812E-03 0.1460724 at 130iterations 3.5493111E-03 8.4622860E-02 at 140iterations 1.9631297E-03 4.1872978E-02 at 150iterations 1.0831837E-03 2.4147987E-02 at 160iterations 5.9864885E-04 1.4877498E-02 at 170iterations 3.2941662E-04 7.8182220E-03 at 180iterations finished qdiffx linear iterations at : 13:25:16 total time elapsed so far: 11.66000 # loops : 180 mean,max change (kT/e) : 3.2941662E-04 7.8182220E-03 energy calculations done at 11.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.83000 DelPhi exited at 13:25:17 11.837u 0.245s 0:12.50 96.5% 0+0k 0+0io 0pf+0w