Sat Oct 8 11:38:17 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 Sat Oct 8 2011 at 11:38:17 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4102 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 0.5249267 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): -3.885000 63.93400 ymin,ymax (A): -12.00100 38.58800 zmin,zma (A): -19.90600 45.38800 x,y,z range (A): 67.81900 50.58900 65.29400 scale (grids/A): 0.5249267 object centre (A): 30.02450 13.29350 12.74100 number of atom coordinates read : 4102 total number of charged atoms : 3950 net assigned charge : -2.485965 assigned positive charge : 614.2223 centred at (gu) : 88.49232 90.20255 90.58931 assigned negative charge : -616.7104 centred at (gu) : 88.47742 90.35705 90.56828 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7150 nv = 96 ne = 84 npr = 85820 no. pairs analyzed = 85820 no. exposed pairs = 4814 no. arc points = 32378 no. surface atoms = 1649 nbur = 2453 mkacc time = 0.1500000 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= 279 mr = 3987 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3266 ## 452 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9616 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2791404E-10 2.6024242E-11 midg,1,midg; midg,igrid,midg 5.2211724E-10 -7.4017331E-10 1,midg,midg; igrid,midg,midg -1.8225291E-10 -2.7384377E-12 gauss-seidel spectral radius is 0.9813812 estimated iterations to convergence 60 setup time was (sec) 0.5600000 now iterating at: 11:38:18 rms-change max change #iterations 7.1969956E-02 9.383991 at 10iterations 5.4243570E-03 0.7979946 at 20iterations 1.0090461E-03 0.1172180 at 30iterations 3.0775936E-04 3.8433075E-02 at 40iterations 9.8867305E-05 1.2891769E-02 at 50iterations finished qdiffx linear iterations at : 11:38:22 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 9.8867305E-05 1.2891769E-02 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 11:38:22 4.373u 0.312s 0:04.98 93.9% 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 Sat Oct 8 2011 at 11:38:22 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4102 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 1.574780 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): -3.885000 63.93400 ymin,ymax (A): -12.00100 38.58800 zmin,zma (A): -19.90600 45.38800 x,y,z range (A): 67.81900 50.58900 65.29400 scale (grids/A): 1.574780 object centre (A): 30.02450 13.29350 12.74100 number of atom coordinates read : 4102 total number of charged atoms : 3950 net assigned charge : -2.485965 assigned positive charge : 614.2223 centred at (gu) : 85.47599 90.60654 91.76669 assigned negative charge : -616.7104 centred at (gu) : 85.43182 91.07088 91.70462 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 81561 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32378 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 25440 mr = 58304 m= 2545 mr = 17968 m= 55 mr = 1234 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 421 time to turn everything in is 0.4200000 number of dielectric boundary points 32093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 410 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 29933 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) : 0.5249267 object centre at (A) : 30.02450 13.29350 12.74100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3761382E-02 -6.4296233E-03 midg,1,midg; midg,igrid,midg 6.2641371E-03 -1.2812671E-02 1,midg,midg; igrid,midg,midg 1.2030425E-02 1.8211020E-02 gauss-seidel spectral radius is 0.9981487 estimated iterations to convergence 185 setup time was (sec) 0.7300000 now iterating at: 11:38:24 rms-change max change #iterations 3.699924 173.8997 at 10iterations 1.526731 52.12108 at 20iterations 0.6317047 23.42963 at 30iterations 0.2616784 8.596466 at 40iterations 0.1088058 4.237144 at 50iterations 4.5220587E-02 1.546335 at 60iterations 1.8797563E-02 0.6147652 at 70iterations 7.9466710E-03 0.2803824 at 80iterations 3.4211196E-03 0.1066438 at 90iterations 1.5496546E-03 5.9435844E-02 at 100iterations 7.6400867E-04 2.6532173E-02 at 110iterations 4.1905930E-04 1.4484406E-02 at 120iterations finished qdiffx linear iterations at : 11:38:33 total time elapsed so far: 10.01000 # loops : 120 mean,max change (kT/e) : 4.1905930E-04 1.4484406E-02 energy calculations done at 10.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.14000 DelPhi exited at 11:38:33 10.141u 0.365s 0:10.93 96.0% 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 8 2011 at 11:38:33 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4102 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 2.362170 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): -3.885000 63.93400 ymin,ymax (A): -12.00100 38.58800 zmin,zma (A): -19.90600 45.38800 x,y,z range (A): 67.81900 50.58900 65.29400 scale (grids/A): 2.362170 object centre (A): 30.02450 13.29350 12.74100 number of atom coordinates read : 4102 total number of charged atoms : 3950 net assigned charge : -2.485965 assigned positive charge : 614.2223 centred at (gu) : 83.21384 90.90961 92.64967 assigned negative charge : -616.7104 centred at (gu) : 83.14753 91.60611 92.55666 start vw surface at 0.1000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 190062 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32378 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 89706 mr = 142376 m= 24705 mr = 72358 m= 3692 mr = 18694 m= 186 mr = 2409 m= 4 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 1324 time to turn everything in is 1.080000 number of dielectric boundary points 72460 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 31533 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) : 1.574780 object centre at (A) : 30.02450 13.29350 12.74100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3528397 -0.1334460 midg,1,midg; midg,igrid,midg 8.3112262E-02 -0.1905390 1,midg,midg; igrid,midg,midg 0.2996374 0.4303960 gauss-seidel spectral radius is 0.9991465 estimated iterations to convergence 270 setup time was (sec) 1.440000 now iterating at: 11:38:35 rms-change max change #iterations 9.716291 318.3868 at 10iterations 5.496950 120.3106 at 20iterations 3.103409 82.61798 at 30iterations 1.740733 38.07986 at 40iterations 0.9682112 19.55991 at 50iterations 0.5391834 10.34075 at 60iterations 0.2996296 5.521742 at 70iterations 0.1658990 3.016106 at 80iterations 9.1875508E-02 1.890404 at 90iterations 5.0974421E-02 0.9760017 at 100iterations 2.8191701E-02 0.5823221 at 110iterations 1.5624943E-02 0.3005657 at 120iterations 8.6654183E-03 0.1673870 at 130iterations 4.8273071E-03 9.2405319E-02 at 140iterations 2.7078288E-03 5.6030273E-02 at 150iterations 1.5348414E-03 2.9243469E-02 at 160iterations 8.9317956E-04 1.7366409E-02 at 170iterations 5.3650909E-04 1.0257721E-02 at 180iterations finished qdiffx linear iterations at : 11:38:51 total time elapsed so far: 16.65000 # loops : 180 mean,max change (kT/e) : 5.3650909E-04 1.0257721E-02 energy calculations done at 16.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.77000 DelPhi exited at 11:38:51 16.774u 0.374s 0:17.50 97.9% 0+0k 0+0io 0pf+0w