Mon Oct 10 19:32:21 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 Mon Oct 10 2011 at 19:32:21 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 = 2938 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: 0.6309931 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): -8.783000 47.63600 ymin,ymax (A): -6.982000 41.94600 zmin,zma (A): 0.7980000 55.51300 x,y,z range (A): 56.41900 48.92800 54.71500 scale (grids/A): 0.6309931 object centre (A): 19.42650 17.48200 28.15550 number of atom coordinates read : 2938 total number of charged atoms : 2796 net assigned charge : -2.499967 assigned positive charge : 440.5220 centred at (gu) : 89.47807 89.69359 88.69527 assigned negative charge : -443.0232 centred at (gu) : 89.45409 89.62358 88.65389 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7913 nv = 96 ne = 84 npr = 58859 no. pairs analyzed = 58859 no. exposed pairs = 3865 no. arc points = 27332 no. surface atoms = 1312 nbur = 1626 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 384 mr = 4166 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3500000 number of dielectric boundary points 4099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2707 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9543 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2997814E-09 1.1531318E-09 midg,1,midg; midg,igrid,midg -1.0691164E-08 4.2040620E-09 1,midg,midg; igrid,midg,midg -5.7970446E-09 -2.0385225E-10 gauss-seidel spectral radius is 0.9870255 estimated iterations to convergence 72 setup time was (sec) 0.6000000 now iterating at: 19:32:22 rms-change max change #iterations 0.1444072 20.49371 at 10iterations 1.3631254E-02 1.857157 at 20iterations 1.3388232E-03 0.1726990 at 30iterations 1.4065177E-04 2.0230293E-02 at 40iterations 2.0179357E-05 3.9825439E-03 at 50iterations finished qdiffx linear iterations at : 19:32:25 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 2.0179357E-05 3.9825439E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 19:32:25 3.570u 0.182s 0:04.27 87.8% 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 Mon Oct 10 2011 at 19:32:25 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 = 2938 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: 1.892979 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): -8.783000 47.63600 ymin,ymax (A): -6.982000 41.94600 zmin,zma (A): 0.7980000 55.51300 x,y,z range (A): 56.41900 48.92800 54.71500 scale (grids/A): 1.892979 object centre (A): 19.42650 17.48200 28.15550 number of atom coordinates read : 2938 total number of charged atoms : 2796 net assigned charge : -2.499967 assigned positive charge : 440.5220 centred at (gu) : 88.43319 89.07988 86.08518 assigned negative charge : -443.0232 centred at (gu) : 88.36201 88.87037 85.96127 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 85526 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27332 grid for indexing accessible points = 1.400000 m= 29076 mr = 58183 m= 4067 mr = 20563 m= 203 mr = 2238 m= 4 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1091 time to turn everything in is 0.6400000 number of dielectric boundary points 37845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21971 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) : 0.6309931 object centre at (A) : 19.42650 17.48200 28.15550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6762929E-02 1.2450323E-02 midg,1,midg; midg,igrid,midg -2.1322090E-02 7.4335095E-03 1,midg,midg; igrid,midg,midg -6.3111261E-02 1.4206434E-02 gauss-seidel spectral radius is 0.9986579 estimated iterations to convergence 216 setup time was (sec) 0.9500000 now iterating at: 19:32:27 rms-change max change #iterations 4.521235 192.8265 at 10iterations 2.116091 67.20668 at 20iterations 0.9977520 30.95846 at 30iterations 0.4686970 13.69845 at 40iterations 0.2211756 6.636290 at 50iterations 0.1039054 3.063314 at 60iterations 4.8940714E-02 1.365189 at 70iterations 2.3079045E-02 0.7048111 at 80iterations 1.0839916E-02 0.3156834 at 90iterations 5.1091639E-03 0.1492748 at 100iterations 2.4163916E-03 6.9713593E-02 at 110iterations 1.1389842E-03 3.2145500E-02 at 120iterations finished qdiffx linear iterations at : 19:32:34 total time elapsed so far: 8.720000 # loops : 120 mean,max change (kT/e) : 1.1389842E-03 3.2145500E-02 energy calculations done at 8.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.910000 DelPhi exited at 19:32:35 8.912u 0.227s 0:09.73 93.8% 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 Mon Oct 10 2011 at 19:32:35 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 = 2938 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: 2.839469 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): -8.783000 47.63600 ymin,ymax (A): -6.982000 41.94600 zmin,zma (A): 0.7980000 55.51300 x,y,z range (A): 56.41900 48.92800 54.71500 scale (grids/A): 2.839469 object centre (A): 19.42650 17.48200 28.15550 number of atom coordinates read : 2938 total number of charged atoms : 2796 net assigned charge : -2.499967 assigned positive charge : 440.5220 centred at (gu) : 87.64970 88.61977 84.12775 assigned negative charge : -443.0232 centred at (gu) : 87.54296 88.30547 83.94177 start vw surface at 0.1700000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 198060 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27332 grid for indexing accessible points = 1.400000 m= 96032 mr = 141796 m= 31988 mr = 76676 m= 6837 mr = 24699 m= 824 mr = 4705 m= 36 mr = 456 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 3531 time to turn everything in is 1.640000 number of dielectric boundary points 85436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 22361 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) : 1.892979 object centre at (A) : 19.42650 17.48200 28.15550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3678604 6.8928272E-02 midg,1,midg; midg,igrid,midg -0.2256104 7.7718586E-02 1,midg,midg; igrid,midg,midg -0.7781077 0.3082457 gauss-seidel spectral radius is 0.9992881 estimated iterations to convergence 296 setup time was (sec) 1.980000 now iterating at: 19:32:37 rms-change max change #iterations 10.82539 328.8216 at 10iterations 6.491992 163.5304 at 20iterations 3.858613 105.0935 at 30iterations 2.281341 55.69810 at 40iterations 1.341527 27.02534 at 50iterations 0.7895291 16.97209 at 60iterations 0.4611585 9.889105 at 70iterations 0.2699375 5.572695 at 80iterations 0.1574682 2.943985 at 90iterations 9.1856390E-02 1.694124 at 100iterations 5.3618535E-02 0.9781494 at 110iterations 3.1208280E-02 0.6634855 at 120iterations 1.8184587E-02 0.3281651 at 130iterations 1.0589548E-02 0.1799116 at 140iterations 6.1532562E-03 0.1031272 at 150iterations 3.5811120E-03 6.3888550E-02 at 160iterations 2.0890424E-03 3.7277222E-02 at 170iterations 1.2138197E-03 2.0732403E-02 at 180iterations finished qdiffx linear iterations at : 19:32:49 total time elapsed so far: 13.43000 # loops : 180 mean,max change (kT/e) : 1.2138197E-03 2.0732403E-02 energy calculations done at 13.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.63000 DelPhi exited at 19:32:50 13.631u 0.227s 0:14.78 93.7% 0+0k 0+0io 0pf+0w