Mon Oct 10 13:59:17 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+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 13:59:17 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7665310 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): -22.76900 23.58000 ymin,ymax (A): -8.192000 36.02200 zmin,zma (A): -3.018000 43.42500 x,y,z range (A): 46.34900 44.21400 46.44300 scale (grids/A): 0.7665310 object centre (A): 0.4055004 13.91500 20.20350 number of atom coordinates read : 2118 total number of charged atoms : 1980 net assigned charge : -3.999990 assigned positive charge : 317.5039 centred at (gu) : 88.91762 90.56841 90.25700 assigned negative charge : -321.5040 centred at (gu) : 88.97330 90.56898 90.42877 start vw surface at 0.1400000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8633 nv = 96 ne = 84 npr = 43673 no. pairs analyzed = 43673 no. exposed pairs = 2659 no. arc points = 18814 no. surface atoms = 910 nbur = 1208 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 628 mr = 4876 m= 3 mr = 135 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 0.3400000 number of dielectric boundary points 4253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1422 ## 135 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8802 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5969276E-07 -4.4313612E-07 midg,1,midg; midg,igrid,midg -1.1031428E-07 -1.3662286E-07 1,midg,midg; igrid,midg,midg -3.1748609E-08 -1.8049788E-07 gauss-seidel spectral radius is 0.9911283 estimated iterations to convergence 86 setup time was (sec) 0.6400000 now iterating at: 13:59:18 rms-change max change #iterations 0.2841111 39.53756 at 10iterations 4.0912744E-02 5.658596 at 20iterations 5.9425728E-03 0.7460289 at 30iterations 8.5688179E-04 9.5609665E-02 at 40iterations 1.2412638E-04 1.6660690E-02 at 50iterations finished qdiffx linear iterations at : 13:59:22 total time elapsed so far: 4.180000 # loops : 50 mean,max change (kT/e) : 1.2412638E-04 1.6660690E-02 energy calculations done at 4.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 13:59:23 4.407u 0.393s 0:05.85 81.8% 0+0k 0+0io 6pf+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 13:59:23 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.299593 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): -22.76900 23.58000 ymin,ymax (A): -8.192000 36.02200 zmin,zma (A): -3.018000 43.42500 x,y,z range (A): 46.34900 44.21400 46.44300 scale (grids/A): 2.299593 object centre (A): 0.4055004 13.91500 20.20350 number of atom coordinates read : 2118 total number of charged atoms : 1980 net assigned charge : -3.999990 assigned positive charge : 317.5039 centred at (gu) : 86.75276 91.70516 90.77101 assigned negative charge : -321.5040 centred at (gu) : 86.92007 91.70686 91.28610 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 90302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18814 grid for indexing accessible points = 1.400000 m= 37793 mr = 62871 m= 8618 mr = 29226 m= 1086 mr = 6067 m= 47 mr = 599 m= 0 mr = 12 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 39071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 15799 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) : 0.7665310 object centre at (A) : 0.4055004 13.91500 20.20350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0815614E-03 -0.1304485 midg,1,midg; midg,igrid,midg -2.8775638E-02 -3.2800999E-02 1,midg,midg; igrid,midg,midg 8.4511880E-03 -1.8958208E-03 gauss-seidel spectral radius is 0.9989857 estimated iterations to convergence 248 setup time was (sec) 1.280000 now iterating at: 13:59:25 rms-change max change #iterations 5.385906 215.7344 at 10iterations 2.792819 85.00350 at 20iterations 1.445623 42.06664 at 30iterations 0.7527924 22.64711 at 40iterations 0.3912448 10.30190 at 50iterations 0.2028525 5.865136 at 60iterations 0.1056138 3.012357 at 70iterations 5.4941677E-02 1.386811 at 80iterations 2.8433330E-02 0.7137804 at 90iterations 1.4819419E-02 0.3808327 at 100iterations 7.7128736E-03 0.1964722 at 110iterations 4.0060403E-03 0.1137314 at 120iterations finished qdiffx linear iterations at : 13:59:35 total time elapsed so far: 11.42000 # loops : 120 mean,max change (kT/e) : 4.0060403E-03 0.1137314 energy calculations done at 11.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 13:59:36 11.636u 0.474s 0:13.03 92.8% 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 13:59:36 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.449389 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): -22.76900 23.58000 ymin,ymax (A): -8.192000 36.02200 zmin,zma (A): -3.018000 43.42500 x,y,z range (A): 46.34900 44.21400 46.44300 scale (grids/A): 3.449389 object centre (A): 0.4055004 13.91500 20.20350 number of atom coordinates read : 2118 total number of charged atoms : 1980 net assigned charge : -3.999990 assigned positive charge : 317.5039 centred at (gu) : 85.12919 92.55771 91.15668 assigned negative charge : -321.5040 centred at (gu) : 85.38012 92.56028 91.92913 start vw surface at 0.1300000 fill in re-entrant regions at 1.210000 boundary points on vw surface= 207389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18814 grid for indexing accessible points = 1.400000 m= 114182 mr = 150709 m= 50697 mr = 95587 m= 16938 mr = 42525 m= 4216 mr = 13479 m= 678 mr = 3223 m= 50 mr = 467 m= 0 mr = 20 time to grow re-entrant surface = 1.610000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.990000 number of dielectric boundary points 88140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 3.150000 number of grid points assigned charge 15840 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) : 2.299593 object centre at (A) : 0.4055004 13.91500 20.20350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0604696E-02 -1.187797 midg,1,midg; midg,igrid,midg -0.2546282 -0.1567825 1,midg,midg; igrid,midg,midg 0.1444567 -0.1006659 gauss-seidel spectral radius is 0.9993336 estimated iterations to convergence 306 setup time was (sec) 3.370000 now iterating at: 13:59:40 rms-change max change #iterations 11.40590 270.9995 at 10iterations 6.776129 115.1947 at 20iterations 4.023947 73.80281 at 30iterations 2.390847 40.10632 at 40iterations 1.413822 22.17035 at 50iterations 0.8357871 12.75000 at 60iterations 0.4946767 7.889166 at 70iterations 0.2924518 4.884171 at 80iterations 0.1729292 2.631685 at 90iterations 0.1023402 1.653933 at 100iterations 6.0430307E-02 0.9915466 at 110iterations 3.5743866E-02 0.6055076 at 120iterations 2.1113735E-02 0.3095388 at 130iterations 1.2479847E-02 0.2002544 at 140iterations 7.3924018E-03 0.1086826 at 150iterations 4.3659005E-03 6.5233231E-02 at 160iterations 2.5795964E-03 4.3285370E-02 at 170iterations 1.5283453E-03 2.7408600E-02 at 180iterations finished qdiffx linear iterations at : 13:59:57 total time elapsed so far: 20.22000 # loops : 180 mean,max change (kT/e) : 1.5283453E-03 2.7408600E-02 energy calculations done at 20.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.43000 DelPhi exited at 13:59:57 20.434u 0.492s 0:21.38 97.8% 0+0k 0+0io 0pf+0w