Mon Oct 10 14:24:50 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 14:24:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 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: 0.5909891 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): -7.579000 44.07400 ymin,ymax (A): 13.12400 73.36200 zmin,zma (A): 55.66800 106.7240 x,y,z range (A): 51.65300 60.23800 51.05600 scale (grids/A): 0.5909891 object centre (A): 18.24750 43.24300 81.19600 number of atom coordinates read : 2622 total number of charged atoms : 2475 net assigned charge : 5.1110983E-06 assigned positive charge : 387.1810 centred at (gu) : 89.97933 90.85722 89.57085 assigned negative charge : -387.1814 centred at (gu) : 89.79717 90.70245 89.63102 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6047 nv = 96 ne = 84 npr = 52695 no. pairs analyzed = 52695 no. exposed pairs = 3509 no. arc points = 24880 no. surface atoms = 1186 nbur = 1436 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 = 1.456000 m= 272 mr = 3039 m= 0 mr = 8 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2425 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7538 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7693945E-09 -1.5375259E-09 midg,1,midg; midg,igrid,midg -3.5693042E-09 5.0530096E-09 1,midg,midg; igrid,midg,midg -5.1664304E-09 4.8277689E-09 gauss-seidel spectral radius is 0.9851912 estimated iterations to convergence 67 setup time was (sec) 0.5600000 now iterating at: 14:24:51 rms-change max change #iterations 9.9527888E-02 16.84544 at 10iterations 8.0743963E-03 1.199587 at 20iterations 6.6415657E-04 0.1202621 at 30iterations 5.3984590E-05 1.0472298E-02 at 40iterations 4.4986336E-06 7.1907043E-04 at 50iterations finished qdiffx linear iterations at : 14:24:54 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 4.4986336E-06 7.1907043E-04 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 14:24:54 3.541u 0.188s 0:04.42 84.1% 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 14:24:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 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: 1.772967 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): -7.579000 44.07400 ymin,ymax (A): 13.12400 73.36200 zmin,zma (A): 55.66800 106.7240 x,y,z range (A): 51.65300 60.23800 51.05600 scale (grids/A): 1.772967 object centre (A): 18.24750 43.24300 81.19600 number of atom coordinates read : 2622 total number of charged atoms : 2475 net assigned charge : 5.1110983E-06 assigned positive charge : 387.1810 centred at (gu) : 89.93729 92.57142 88.71226 assigned negative charge : -387.1814 centred at (gu) : 89.39121 92.10690 88.89270 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 66195 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24880 grid for indexing accessible points = 1.400000 m= 20873 mr = 44153 m= 2281 mr = 13932 m= 111 mr = 987 m= 0 mr = 20 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 30368 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 212 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19251 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) : 0.5909891 object centre at (A) : 18.24750 43.24300 81.19600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8488216E-03 1.5153607E-03 midg,1,midg; midg,igrid,midg -6.4436342E-03 1.1933614E-02 1,midg,midg; igrid,midg,midg -2.3657175E-02 7.7313809E-03 gauss-seidel spectral radius is 0.9984345 estimated iterations to convergence 201 setup time was (sec) 0.8300000 now iterating at: 14:24:56 rms-change max change #iterations 3.672767 174.3349 at 10iterations 1.612961 60.41936 at 20iterations 0.7181507 25.51144 at 30iterations 0.3169682 11.84837 at 40iterations 0.1400829 5.070457 at 50iterations 6.2321723E-02 2.359222 at 60iterations 2.7660929E-02 0.9187746 at 70iterations 1.2238008E-02 0.4091444 at 80iterations 5.4386524E-03 0.2063522 at 90iterations 2.4125488E-03 9.5840454E-02 at 100iterations 1.0727239E-03 3.8748741E-02 at 110iterations 4.7625659E-04 1.6805649E-02 at 120iterations finished qdiffx linear iterations at : 14:25:02 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 4.7625659E-04 1.6805649E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 14:25:03 7.898u 0.214s 0:08.45 95.8% 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 14:25:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 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: 2.659451 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): -7.579000 44.07400 ymin,ymax (A): 13.12400 73.36200 zmin,zma (A): 55.66800 106.7240 x,y,z range (A): 51.65300 60.23800 51.05600 scale (grids/A): 2.659451 object centre (A): 18.24750 43.24300 81.19600 number of atom coordinates read : 2622 total number of charged atoms : 2475 net assigned charge : 5.1110983E-06 assigned positive charge : 387.1810 centred at (gu) : 89.90598 93.85683 88.06837 assigned negative charge : -387.1814 centred at (gu) : 89.08669 93.16031 88.33894 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 153237 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24880 grid for indexing accessible points = 1.400000 m= 70781 mr = 107784 m= 21007 mr = 55240 m= 3383 mr = 15165 m= 312 mr = 2039 m= 12 mr = 137 m= 0 mr = 6 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 68361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 19794 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) : 1.772967 object centre at (A) : 18.24750 43.24300 81.19600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2013468 2.3507800E-02 midg,1,midg; midg,igrid,midg -7.0196927E-02 3.1052193E-02 1,midg,midg; igrid,midg,midg -0.3049014 5.2678138E-02 gauss-seidel spectral radius is 0.9992114 estimated iterations to convergence 281 setup time was (sec) 1.580000 now iterating at: 14:25:05 rms-change max change #iterations 9.127900 316.9040 at 10iterations 5.323053 129.9581 at 20iterations 3.055886 73.83560 at 30iterations 1.748583 40.93689 at 40iterations 1.000128 22.23890 at 50iterations 0.5697143 12.93345 at 60iterations 0.3225359 7.661041 at 70iterations 0.1830182 4.038877 at 80iterations 0.1035629 2.292196 at 90iterations 5.8698922E-02 1.232454 at 100iterations 3.3213831E-02 0.7071266 at 110iterations 1.8769354E-02 0.3722401 at 120iterations 1.0602395E-02 0.2193756 at 130iterations 5.9891324E-03 0.1161041 at 140iterations 3.3818439E-03 7.0581675E-02 at 150iterations 1.9070590E-03 3.9655209E-02 at 160iterations 1.0769146E-03 2.0547390E-02 at 170iterations 6.0702109E-04 1.1105537E-02 at 180iterations finished qdiffx linear iterations at : 14:25:16 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 6.0702109E-04 1.1105537E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 14:25:16 12.783u 0.217s 0:13.39 97.0% 0+0k 0+0io 0pf+0w