Mon Oct 10 13:58:40 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+sph2.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 = amb2.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 13:58:40 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: GLM 85 has a net charge of -0.0940 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 0.5715938 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): -16.68300 32.43000 ymin,ymax (A): 17.70400 79.98600 zmin,zma (A): 31.37100 84.69500 x,y,z range (A): 49.11300 62.28200 53.32400 scale (grids/A): 0.5715938 object centre (A): 7.873500 48.84500 58.03300 number of atom coordinates read : 2785 total number of charged atoms : 2639 net assigned charge : 3.877032 assigned positive charge : 407.3015 centred at (gu) : 90.74391 89.32740 91.78386 assigned negative charge : -403.4256 centred at (gu) : 90.68400 89.38346 91.89999 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6061 nv = 96 ne = 84 npr = 55932 no. pairs analyzed = 55932 no. exposed pairs = 3649 no. arc points = 25349 no. surface atoms = 1228 nbur = 1557 mkacc time = 0.1200000 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= 302 mr = 3148 m= 0 mr = 9 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2525 ## 264 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7660 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5530779E-09 -1.7457923E-09 midg,1,midg; midg,igrid,midg 1.7407116E-09 -1.6276633E-10 1,midg,midg; igrid,midg,midg -2.0849028E-10 1.8387495E-09 gauss-seidel spectral radius is 0.9841942 estimated iterations to convergence 65 setup time was (sec) 0.5200000 now iterating at: 13:58:40 rms-change max change #iterations 8.9291148E-02 14.42586 at 10iterations 6.6520316E-03 1.262440 at 20iterations 5.0597382E-04 7.9078674E-02 at 30iterations 3.7425973E-05 5.1803589E-03 at 40iterations 2.9469322E-06 5.8078766E-04 at 50iterations finished qdiffx linear iterations at : 13:58:43 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 2.9469322E-06 5.8078766E-04 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 13:58:44 3.063u 0.154s 0:03.69 86.9% 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 Mon Oct 10 2011 at 13:58:44 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: GLM 85 has a net charge of -0.0940 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 1.714781 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): -16.68300 32.43000 ymin,ymax (A): 17.70400 79.98600 zmin,zma (A): 31.37100 84.69500 x,y,z range (A): 49.11300 62.28200 53.32400 scale (grids/A): 1.714781 object centre (A): 7.873500 48.84500 58.03300 number of atom coordinates read : 2785 total number of charged atoms : 2639 net assigned charge : 3.877032 assigned positive charge : 407.3015 centred at (gu) : 92.23098 87.98196 95.35101 assigned negative charge : -403.4256 centred at (gu) : 92.05180 88.15034 95.69988 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66164 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25349 grid for indexing accessible points = 1.400000 m= 22334 mr = 44561 m= 2877 mr = 15660 m= 96 mr = 1529 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 79 time to turn everything in is 0.4600000 number of dielectric boundary points 29716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 20380 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) : 0.5715938 object centre at (A) : 7.873500 48.84500 58.03300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0349436E-02 -2.1246898E-03 midg,1,midg; midg,igrid,midg 3.7368733E-02 1.6860947E-02 1,midg,midg; igrid,midg,midg -4.9066702E-03 2.1315110E-03 gauss-seidel spectral radius is 0.9983409 estimated iterations to convergence 195 setup time was (sec) 0.7300000 now iterating at: 13:58:44 rms-change max change #iterations 3.529792 155.7299 at 10iterations 1.518499 56.23451 at 20iterations 0.6580814 27.63910 at 30iterations 0.2846690 11.60381 at 40iterations 0.1224492 4.600749 at 50iterations 5.3061247E-02 1.888401 at 60iterations 2.3043808E-02 0.8670864 at 70iterations 1.0003162E-02 0.3637953 at 80iterations 4.3294285E-03 0.1463761 at 90iterations 1.8750264E-03 5.7241440E-02 at 100iterations 8.1705279E-04 3.0750275E-02 at 110iterations 3.5335464E-04 1.2062423E-02 at 120iterations finished qdiffx linear iterations at : 13:58:51 total time elapsed so far: 6.770000 # loops : 120 mean,max change (kT/e) : 3.5335464E-04 1.2062423E-02 energy calculations done at 6.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 13:58:51 6.951u 0.153s 0:07.46 95.1% 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 13:58:51 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: GLM 85 has a net charge of -0.0940 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 2.572172 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): -16.68300 32.43000 ymin,ymax (A): 17.70400 79.98600 zmin,zma (A): 31.37100 84.69500 x,y,z range (A): 49.11300 62.28200 53.32400 scale (grids/A): 2.572172 object centre (A): 7.873500 48.84500 58.03300 number of atom coordinates read : 2785 total number of charged atoms : 2639 net assigned charge : 3.877032 assigned positive charge : 407.3015 centred at (gu) : 93.34635 86.97272 98.02639 assigned negative charge : -403.4256 centred at (gu) : 93.07766 87.22540 98.54967 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 153469 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25349 grid for indexing accessible points = 1.400000 m= 73660 mr = 108998 m= 24453 mr = 58330 m= 4740 mr = 18771 m= 355 mr = 3189 m= 9 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 296 time to turn everything in is 1.180000 number of dielectric boundary points 67257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 21088 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) : 1.714781 object centre at (A) : 7.873500 48.84500 58.03300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3328036 -4.4669654E-02 midg,1,midg; midg,igrid,midg 0.6776789 0.4769534 1,midg,midg; igrid,midg,midg -4.1642636E-02 2.7607799E-02 gauss-seidel spectral radius is 0.9991829 estimated iterations to convergence 276 setup time was (sec) 1.460000 now iterating at: 13:58:53 rms-change max change #iterations 8.849981 265.2288 at 10iterations 5.052763 126.0586 at 20iterations 2.855963 66.01134 at 30iterations 1.609483 34.03587 at 40iterations 0.9019513 19.49991 at 50iterations 0.5049231 11.03122 at 60iterations 0.2827360 5.991448 at 70iterations 0.1576322 3.470345 at 80iterations 8.8221848E-02 1.749975 at 90iterations 4.9238782E-02 0.9486732 at 100iterations 2.7466865E-02 0.5205803 at 110iterations 1.5333111E-02 0.3259239 at 120iterations 8.5564787E-03 0.1666718 at 130iterations 4.7677332E-03 9.9096298E-02 at 140iterations 2.6547767E-03 5.2270889E-02 at 150iterations 1.4843699E-03 2.7736664E-02 at 160iterations 8.2811929E-04 1.5959740E-02 at 170iterations 4.5992160E-04 9.6254349E-03 at 180iterations finished qdiffx linear iterations at : 13:59:02 total time elapsed so far: 10.62000 # loops : 180 mean,max change (kT/e) : 4.5992160E-04 9.6254349E-03 energy calculations done at 10.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.79000 DelPhi exited at 13:59:03 10.793u 0.188s 0:11.82 92.8% 0+0k 0+0io 0pf+0w