Tue Oct 11 03:17:37 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 03:17:37 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3159 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: 0.5508277 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): -8.882999 52.00400 ymin,ymax (A): 18.91200 67.70900 zmin,zma (A): -4.259000 60.37100 x,y,z range (A): 60.88700 48.79700 64.63000 scale (grids/A): 0.5508277 object centre (A): 21.56050 43.31050 28.05600 number of atom coordinates read : 3159 total number of charged atoms : 3000 net assigned charge : 7.500019 assigned positive charge : 471.4066 centred at (gu) : 90.94547 90.92435 87.49757 assigned negative charge : -463.9081 centred at (gu) : 90.94638 90.85138 87.38592 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6366 nv = 96 ne = 84 npr = 60401 no. pairs analyzed = 60401 no. exposed pairs = 4712 no. arc points = 33068 no. surface atoms = 1547 nbur = 1612 mkacc time = 0.1300000 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 = 1.540000 m= 328 mr = 2936 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3171 ## 384 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8155 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9481843E-10 8.0997253E-10 midg,1,midg; midg,igrid,midg -1.5938357E-11 1.4707061E-09 1,midg,midg; igrid,midg,midg 4.6825827E-10 7.1610651E-10 gauss-seidel spectral radius is 0.9830327 estimated iterations to convergence 63 setup time was (sec) 0.5700000 now iterating at: 03:17:38 rms-change max change #iterations 8.0273904E-02 15.47399 at 10iterations 5.4746456E-03 0.8691869 at 20iterations 4.0208307E-04 7.2648048E-02 at 30iterations 5.3192027E-05 8.7509155E-03 at 40iterations 1.2796029E-05 2.3183823E-03 at 50iterations finished qdiffx linear iterations at : 03:17:40 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.2796029E-05 2.3183823E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 03:17:41 3.341u 0.205s 0:03.89 91.0% 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 Tue Oct 11 2011 at 03:17:41 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3159 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: 1.652483 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): -8.882999 52.00400 ymin,ymax (A): 18.91200 67.70900 zmin,zma (A): -4.259000 60.37100 x,y,z range (A): 60.88700 48.79700 64.63000 scale (grids/A): 1.652483 object centre (A): 21.56050 43.31050 28.05600 number of atom coordinates read : 3159 total number of charged atoms : 3000 net assigned charge : 7.500019 assigned positive charge : 471.4066 centred at (gu) : 92.83556 92.77216 82.49182 assigned negative charge : -463.9081 centred at (gu) : 92.83858 92.55389 82.15722 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68701 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33068 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 21901 mr = 42916 m= 2966 mr = 14372 m= 119 mr = 1541 m= 0 mr = 12 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 186 time to turn everything in is 0.5000000 number of dielectric boundary points 34846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 311 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 22975 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) : 0.5508277 object centre at (A) : 21.56050 43.31050 28.05600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6078282E-02 2.1508051E-02 midg,1,midg; midg,igrid,midg 5.5407587E-04 6.7141200E-03 1,midg,midg; igrid,midg,midg -6.5917731E-03 -6.2155956E-03 gauss-seidel spectral radius is 0.9982700 estimated iterations to convergence 191 setup time was (sec) 0.7800000 now iterating at: 03:17:42 rms-change max change #iterations 3.524550 153.9790 at 10iterations 1.496715 53.69482 at 20iterations 0.6349810 27.19486 at 30iterations 0.2704098 9.593933 at 40iterations 0.1145532 4.095772 at 50iterations 4.8932415E-02 1.729016 at 60iterations 2.0741163E-02 0.7767181 at 70iterations 8.8671781E-03 0.3107581 at 80iterations 3.7551131E-03 0.1225841 at 90iterations 1.6030287E-03 5.6297302E-02 at 100iterations 6.8134215E-04 2.4790764E-02 at 110iterations 2.9175141E-04 1.0620117E-02 at 120iterations finished qdiffx linear iterations at : 03:17:48 total time elapsed so far: 7.200000 # loops : 120 mean,max change (kT/e) : 2.9175141E-04 1.0620117E-02 energy calculations done at 7.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 03:17:49 7.379u 0.233s 0:07.91 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 Tue Oct 11 2011 at 03:17:49 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3159 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: 2.478725 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): -8.882999 52.00400 ymin,ymax (A): 18.91200 67.70900 zmin,zma (A): -4.259000 60.37100 x,y,z range (A): 60.88700 48.79700 64.63000 scale (grids/A): 2.478725 object centre (A): 21.56050 43.31050 28.05600 number of atom coordinates read : 3159 total number of charged atoms : 3000 net assigned charge : 7.500019 assigned positive charge : 471.4066 centred at (gu) : 94.25313 94.15807 78.73755 assigned negative charge : -463.9081 centred at (gu) : 94.25795 93.83069 78.23560 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 158647 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33068 grid for indexing accessible points = 1.400000 m= 72347 mr = 105746 m= 23378 mr = 54693 m= 4904 mr = 17139 m= 515 mr = 3342 m= 11 mr = 265 m= 0 mr = 1 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 640 time to turn everything in is 1.190000 number of dielectric boundary points 78616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 23970 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) : 1.652483 object centre at (A) : 21.56050 43.31050 28.05600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6700016 0.2769199 midg,1,midg; midg,igrid,midg 1.3154805E-02 6.1590023E-02 1,midg,midg; igrid,midg,midg -7.1257316E-02 -0.3064112 gauss-seidel spectral radius is 0.9991848 estimated iterations to convergence 277 setup time was (sec) 1.500000 now iterating at: 03:17:50 rms-change max change #iterations 9.221838 344.2090 at 10iterations 5.334826 126.4702 at 20iterations 3.058104 87.05791 at 30iterations 1.738304 44.15889 at 40iterations 0.9877837 20.56931 at 50iterations 0.5594884 12.39771 at 60iterations 0.3149979 6.927900 at 70iterations 0.1776325 3.600470 at 80iterations 9.9768825E-02 2.013103 at 90iterations 5.5928729E-02 1.245270 at 100iterations 3.1477947E-02 0.6614785 at 110iterations 1.7612614E-02 0.3530540 at 120iterations 9.8750377E-03 0.2058029 at 130iterations 5.5280281E-03 0.1122389 at 140iterations 3.0914166E-03 6.5704346E-02 at 150iterations 1.7336064E-03 3.5099983E-02 at 160iterations 9.7193872E-04 1.8436432E-02 at 170iterations 5.4628513E-04 1.1396885E-02 at 180iterations finished qdiffx linear iterations at : 03:18:01 total time elapsed so far: 11.90000 # loops : 180 mean,max change (kT/e) : 5.4628513E-04 1.1396885E-02 energy calculations done at 11.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 03:18:01 12.073u 0.247s 0:12.69 97.0% 0+0k 0+0io 0pf+0w