Mon Oct 10 14:07:54 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 14:07:55 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3291 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: 0.5383417 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): -9.565001 47.82000 ymin,ymax (A): -19.33600 35.64300 zmin,zma (A): -24.64800 41.48100 x,y,z range (A): 57.38500 54.97900 66.12901 scale (grids/A): 0.5383417 object centre (A): 19.12750 8.153499 8.416501 number of atom coordinates read : 3291 total number of charged atoms : 3153 net assigned charge : 0.5000058 assigned positive charge : 501.6565 centred at (gu) : 88.33568 87.98422 90.74146 assigned negative charge : -501.1578 centred at (gu) : 88.26221 88.03110 90.62450 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6121 nv = 96 ne = 84 npr = 66987 no. pairs analyzed = 66987 no. exposed pairs = 4396 no. arc points = 30565 no. surface atoms = 1463 nbur = 1828 mkacc time = 0.1400000 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 = 1.596000 m= 244 mr = 2988 m= 0 mr = 6 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3107 ## 409 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8149 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2974919E-10 7.9745732E-10 midg,1,midg; midg,igrid,midg 4.6781012E-10 -1.4545533E-10 1,midg,midg; igrid,midg,midg -6.0304761E-10 2.7888025E-10 gauss-seidel spectral radius is 0.9822414 estimated iterations to convergence 62 setup time was (sec) 0.5700000 now iterating at: 14:07:55 rms-change max change #iterations 7.2964102E-02 12.90888 at 10iterations 4.8713991E-03 0.8298302 at 20iterations 4.2240074E-04 0.1013260 at 30iterations 5.8852340E-05 9.5481873E-03 at 40iterations 1.0586433E-05 1.7871857E-03 at 50iterations finished qdiffx linear iterations at : 14:07:58 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.0586433E-05 1.7871857E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 14:07:59 3.371u 0.186s 0:04.16 85.3% 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 14:07:59 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3291 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: 1.615025 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): -9.565001 47.82000 ymin,ymax (A): -19.33600 35.64300 zmin,zma (A): -24.64800 41.48100 x,y,z range (A): 57.38500 54.97900 66.12901 scale (grids/A): 1.615025 object centre (A): 19.12750 8.153499 8.416501 number of atom coordinates read : 3291 total number of charged atoms : 3153 net assigned charge : 0.5000058 assigned positive charge : 501.6565 centred at (gu) : 85.00632 83.95190 92.22326 assigned negative charge : -501.1578 centred at (gu) : 84.78642 84.09277 91.87309 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 68377 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30565 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20075 mr = 45343 m= 2122 mr = 13181 m= 65 mr = 981 m= 0 mr = 4 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 275 time to turn everything in is 0.5400000 number of dielectric boundary points 31130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 324 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 24072 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) : 0.5383417 object centre at (A) : 19.12750 8.153499 8.416501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0736525E-03 2.5612015E-02 midg,1,midg; midg,igrid,midg -8.5953390E-03 -1.0143035E-02 1,midg,midg; igrid,midg,midg -1.4546467E-02 8.5248903E-04 gauss-seidel spectral radius is 0.9981757 estimated iterations to convergence 186 setup time was (sec) 0.8400000 now iterating at: 14:08:00 rms-change max change #iterations 3.470216 161.8358 at 10iterations 1.444228 67.58406 at 20iterations 0.5983004 21.11236 at 30iterations 0.2488250 8.720950 at 40iterations 0.1034335 3.701611 at 50iterations 4.3061763E-02 1.542521 at 60iterations 1.7904522E-02 0.6539207 at 70iterations 7.4890051E-03 0.2661667 at 80iterations 3.1303286E-03 0.1151304 at 90iterations 1.3066211E-03 5.0411224E-02 at 100iterations 5.5038149E-04 1.9012451E-02 at 110iterations 2.3192541E-04 8.0299377E-03 at 120iterations finished qdiffx linear iterations at : 14:08:06 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 2.3192541E-04 8.0299377E-03 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 14:08:07 7.539u 0.237s 0:08.54 90.8% 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 14:08:07 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3291 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: 2.422538 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): -9.565001 47.82000 ymin,ymax (A): -19.33600 35.64300 zmin,zma (A): -24.64800 41.48100 x,y,z range (A): 57.38500 54.97900 66.12901 scale (grids/A): 2.422538 object centre (A): 19.12750 8.153499 8.416501 number of atom coordinates read : 3291 total number of charged atoms : 3153 net assigned charge : 0.5000058 assigned positive charge : 501.6565 centred at (gu) : 82.50922 80.92775 93.33475 assigned negative charge : -501.1578 centred at (gu) : 82.17948 81.13889 92.80957 start vw surface at 0.1600000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 158928 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30565 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 70438 mr = 111830 m= 19296 mr = 54143 m= 3332 mr = 13757 m= 252 mr = 2155 m= 3 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 889 time to turn everything in is 1.180000 number of dielectric boundary points 70274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 25189 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) : 1.615025 object centre at (A) : 19.12750 8.153499 8.416501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1471356E-02 0.3177994 midg,1,midg; midg,igrid,midg -0.2158653 -0.1747925 1,midg,midg; igrid,midg,midg -0.1990720 -2.9394860E-04 gauss-seidel spectral radius is 0.9991397 estimated iterations to convergence 269 setup time was (sec) 1.490000 now iterating at: 14:08:09 rms-change max change #iterations 9.096449 302.2243 at 10iterations 5.122611 124.5531 at 20iterations 2.873756 74.72911 at 30iterations 1.597386 33.90261 at 40iterations 0.8889260 18.54657 at 50iterations 0.4922375 10.63077 at 60iterations 0.2720285 5.878349 at 70iterations 0.1498065 3.163268 at 80iterations 8.2661144E-02 1.699749 at 90iterations 4.5518234E-02 1.039632 at 100iterations 2.5086157E-02 0.5201600 at 110iterations 1.3819855E-02 0.2800102 at 120iterations 7.5931875E-03 0.1609048 at 130iterations 4.1855094E-03 8.7009430E-02 at 140iterations 2.3114420E-03 4.6729565E-02 at 150iterations 1.2688820E-03 2.5733948E-02 at 160iterations 7.0126803E-04 1.4495850E-02 at 170iterations 3.8834155E-04 7.8239441E-03 at 180iterations finished qdiffx linear iterations at : 14:08:20 total time elapsed so far: 11.87000 # loops : 180 mean,max change (kT/e) : 3.8834155E-04 7.8239441E-03 energy calculations done at 11.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.04000 DelPhi exited at 14:08:20 12.047u 0.221s 0:12.60 97.3% 0+0k 0+0io 0pf+0w