Tue Oct 11 03:17:48 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 Tue Oct 11 2011 at 03:17:48 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3332 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: 0.5384068 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): 19.64000 85.76100 ymin,ymax (A): 80.27600 134.1930 zmin,zma (A): 3.866000 52.91300 x,y,z range (A): 66.12100 53.91699 49.04700 scale (grids/A): 0.5384068 object centre (A): 52.70050 107.2345 28.38950 number of atom coordinates read : 3332 total number of charged atoms : 3185 net assigned charge : -10.49998 assigned positive charge : 500.5332 centred at (gu) : 90.08815 89.99164 89.90383 assigned negative charge : -511.0345 centred at (gu) : 90.06989 89.80653 90.03162 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6325 nv = 96 ne = 84 npr = 65763 no. pairs analyzed = 65763 no. exposed pairs = 4401 no. arc points = 30946 no. surface atoms = 1453 nbur = 1879 mkacc time = 0.1600000 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 = 1.568000 m= 265 mr = 3233 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.3600000 number of dielectric boundary points 3342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3115 ## 444 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8352 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4417232E-10 -1.1997622E-09 midg,1,midg; midg,igrid,midg -1.5746724E-09 5.5256749E-10 1,midg,midg; igrid,midg,midg -5.7614929E-10 -3.8725520E-10 gauss-seidel spectral radius is 0.9822516 estimated iterations to convergence 62 setup time was (sec) 0.6300000 now iterating at: 03:17:48 rms-change max change #iterations 7.2901793E-02 12.03244 at 10iterations 5.0025671E-03 0.7560978 at 20iterations 5.4056977E-04 0.1360645 at 30iterations 1.3210150E-04 3.8604736E-02 at 40iterations 3.7551570E-05 1.1121750E-02 at 50iterations finished qdiffx linear iterations at : 03:17:51 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 3.7551570E-05 1.1121750E-02 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 03:17:52 3.685u 0.184s 0:04.17 92.5% 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 Tue Oct 11 2011 at 03:17:52 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3332 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.615221 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): 19.64000 85.76100 ymin,ymax (A): 80.27600 134.1930 zmin,zma (A): 3.866000 52.91300 x,y,z range (A): 66.12100 53.91699 49.04700 scale (grids/A): 1.615221 object centre (A): 52.70050 107.2345 28.38950 number of atom coordinates read : 3332 total number of charged atoms : 3185 net assigned charge : -10.49998 assigned positive charge : 500.5332 centred at (gu) : 90.26361 89.97354 89.71010 assigned negative charge : -511.0345 centred at (gu) : 90.20918 89.41889 90.09421 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 70472 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30946 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21206 mr = 47454 m= 2119 mr = 14382 m= 56 mr = 1074 m= 0 mr = 4 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 3481 time to turn everything in is 0.5500000 number of dielectric boundary points 30939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 389 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 24347 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) : 0.5384068 object centre at (A) : 52.70050 107.2345 28.38950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9376391E-04 -1.0576298E-02 midg,1,midg; midg,igrid,midg -2.5790559E-02 5.1042996E-04 1,midg,midg; igrid,midg,midg -1.0474478E-02 -5.6067305E-03 gauss-seidel spectral radius is 0.9981868 estimated iterations to convergence 187 setup time was (sec) 0.8600000 now iterating at: 03:17:53 rms-change max change #iterations 3.491920 158.4394 at 10iterations 1.442242 57.18861 at 20iterations 0.6016209 21.73555 at 30iterations 0.2503193 8.625263 at 40iterations 0.1043616 3.573918 at 50iterations 4.3590806E-02 1.444287 at 60iterations 1.8279992E-02 0.6561909 at 70iterations 7.6509817E-03 0.2609291 at 80iterations 3.1899177E-03 0.1079054 at 90iterations 1.3609519E-03 5.1746368E-02 at 100iterations 5.9426384E-04 2.3635864E-02 at 110iterations 2.7081138E-04 1.1718750E-02 at 120iterations finished qdiffx linear iterations at : 03:18:00 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 2.7081138E-04 1.1718750E-02 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 03:18:01 8.300u 0.243s 0:08.83 96.7% 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 Tue Oct 11 2011 at 03:18:01 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3332 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.422831 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): 19.64000 85.76100 ymin,ymax (A): 80.27600 134.1930 zmin,zma (A): 3.866000 52.91300 x,y,z range (A): 66.12100 53.91699 49.04700 scale (grids/A): 2.422831 object centre (A): 52.70050 107.2345 28.38950 number of atom coordinates read : 3332 total number of charged atoms : 3185 net assigned charge : -10.49998 assigned positive charge : 500.5332 centred at (gu) : 90.39518 89.96019 89.56516 assigned negative charge : -511.0345 centred at (gu) : 90.31364 89.12822 90.14138 start vw surface at 0.1800000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 163727 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30946 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 73808 mr = 116419 m= 20577 mr = 57756 m= 3362 mr = 15378 m= 228 mr = 2215 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 11582 time to turn everything in is 1.270000 number of dielectric boundary points 69855 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 25435 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) : 1.615221 object centre at (A) : 52.70050 107.2345 28.38950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1253670E-02 -0.1410818 midg,1,midg; midg,igrid,midg -0.3791940 1.3420820E-02 1,midg,midg; igrid,midg,midg -0.1419600 -1.9075317E-02 gauss-seidel spectral radius is 0.9991490 estimated iterations to convergence 271 setup time was (sec) 1.620000 now iterating at: 03:18:03 rms-change max change #iterations 9.114171 315.4709 at 10iterations 5.120065 151.2803 at 20iterations 2.868312 62.26714 at 30iterations 1.597879 35.11957 at 40iterations 0.8854855 19.33089 at 50iterations 0.4910648 10.40223 at 60iterations 0.2717691 5.338783 at 70iterations 0.1505496 3.094579 at 80iterations 8.3124377E-02 1.673518 at 90iterations 4.5940403E-02 0.9757309 at 100iterations 2.5317073E-02 0.5655441 at 110iterations 1.3986701E-02 0.3106387 at 120iterations 7.7286134E-03 0.1560326 at 130iterations 4.2702714E-03 8.4760666E-02 at 140iterations 2.3672928E-03 4.8841238E-02 at 150iterations 1.3185771E-03 2.8831482E-02 at 160iterations 7.3969632E-04 1.7314911E-02 at 170iterations 4.2089727E-04 1.0349274E-02 at 180iterations finished qdiffx linear iterations at : 03:18:14 total time elapsed so far: 12.83000 # loops : 180 mean,max change (kT/e) : 4.2089727E-04 1.0349274E-02 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 03:18:14 13.018u 0.238s 0:13.59 97.4% 0+0k 0+0io 0pf+0w