Sun Oct 9 21:06:57 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 Sun Oct 9 2011 at 21:06:57 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3174 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: 0.6086615 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): -21.12900 31.92400 ymin,ymax (A): 23.39400 81.88300 zmin,zma (A): -16.71700 38.42100 x,y,z range (A): 53.05300 58.48899 55.13800 scale (grids/A): 0.6086615 object centre (A): 5.397500 52.63850 10.85200 number of atom coordinates read : 3174 total number of charged atoms : 3026 net assigned charge : 4.500013 assigned positive charge : 479.6007 centred at (gu) : 89.09372 88.15614 89.20749 assigned negative charge : -475.1020 centred at (gu) : 89.17020 88.11508 89.15704 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7884 nv = 96 ne = 84 npr = 62534 no. pairs analyzed = 62534 no. exposed pairs = 4284 no. arc points = 31024 no. surface atoms = 1428 nbur = 1746 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 422 mr = 3961 m= 3 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3160 ## 342 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9867 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7395621E-10 4.5872830E-09 midg,1,midg; midg,igrid,midg 1.8616940E-10 3.2881595E-09 1,midg,midg; igrid,midg,midg 8.5282954E-09 -1.5247259E-09 gauss-seidel spectral radius is 0.9860862 estimated iterations to convergence 69 setup time was (sec) 0.6400000 now iterating at: 21:06:58 rms-change max change #iterations 0.1273055 18.73974 at 10iterations 1.1145998E-02 1.724143 at 20iterations 9.9605031E-04 0.1374874 at 30iterations 9.1844413E-05 1.3428211E-02 at 40iterations 1.1403880E-05 1.7108917E-03 at 50iterations finished qdiffx linear iterations at : 21:07:02 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 1.1403880E-05 1.7108917E-03 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.580000 DelPhi exited at 21:07:02 4.580u 0.373s 0:05.23 94.6% 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 Sun Oct 9 2011 at 21:07:02 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3174 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: 1.825985 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): -21.12900 31.92400 ymin,ymax (A): 23.39400 81.88300 zmin,zma (A): -16.71700 38.42100 x,y,z range (A): 53.05300 58.48899 55.13800 scale (grids/A): 1.825985 object centre (A): 5.397500 52.63850 10.85200 number of atom coordinates read : 3174 total number of charged atoms : 3026 net assigned charge : 4.500013 assigned positive charge : 479.6007 centred at (gu) : 87.28006 84.46761 87.62138 assigned negative charge : -475.1020 centred at (gu) : 87.51028 84.34503 87.47067 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 85605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31024 grid for indexing accessible points = 1.400000 m= 28320 mr = 56496 m= 3983 mr = 19592 m= 214 mr = 2256 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 288 time to turn everything in is 0.7200000 number of dielectric boundary points 39722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 23655 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) : 0.6086615 object centre at (A) : 5.397500 52.63850 10.85200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3695315E-02 1.6311820E-03 midg,1,midg; midg,igrid,midg 3.4452334E-02 5.5927122E-03 1,midg,midg; igrid,midg,midg 1.4619843E-02 -1.7018522E-03 gauss-seidel spectral radius is 0.9985920 estimated iterations to convergence 211 setup time was (sec) 1.050000 now iterating at: 21:07:04 rms-change max change #iterations 4.345401 162.0357 at 10iterations 2.004439 67.55234 at 20iterations 0.9251728 28.71737 at 30iterations 0.4262177 12.89152 at 40iterations 0.1967762 5.905960 at 50iterations 9.0873137E-02 2.780823 at 60iterations 4.1892335E-02 1.265469 at 70iterations 1.9433474E-02 0.6037036 at 80iterations 8.9868419E-03 0.2895565 at 90iterations 4.1548098E-03 0.1222572 at 100iterations 1.9168772E-03 5.5763245E-02 at 110iterations 8.9078676E-04 2.8617859E-02 at 120iterations finished qdiffx linear iterations at : 21:07:14 total time elapsed so far: 10.95000 # loops : 120 mean,max change (kT/e) : 8.9078676E-04 2.8617859E-02 energy calculations done at 10.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.11000 DelPhi exited at 21:07:14 11.118u 0.454s 0:11.94 96.8% 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 Sun Oct 9 2011 at 21:07:14 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3174 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: 2.738977 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): -21.12900 31.92400 ymin,ymax (A): 23.39400 81.88300 zmin,zma (A): -16.71700 38.42100 x,y,z range (A): 53.05300 58.48899 55.13800 scale (grids/A): 2.738977 object centre (A): 5.397500 52.63850 10.85200 number of atom coordinates read : 3174 total number of charged atoms : 3026 net assigned charge : 4.500013 assigned positive charge : 479.6007 centred at (gu) : 85.91992 81.70105 86.43195 assigned negative charge : -475.1020 centred at (gu) : 86.26530 81.51738 86.20605 start vw surface at 0.1400000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 198282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31024 grid for indexing accessible points = 1.400000 m= 93536 mr = 138570 m= 30883 mr = 73547 m= 6878 mr = 23394 m= 928 mr = 4846 m= 45 mr = 598 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 1152 time to turn everything in is 1.790000 number of dielectric boundary points 89593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 24199 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) : 1.825985 object centre at (A) : 5.397500 52.63850 10.85200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3188785 -1.3043744E-03 midg,1,midg; midg,igrid,midg 0.9733362 0.1462491 1,midg,midg; igrid,midg,midg 0.2202156 -3.8426861E-02 gauss-seidel spectral radius is 0.9992763 estimated iterations to convergence 293 setup time was (sec) 2.150000 now iterating at: 21:07:17 rms-change max change #iterations 10.67737 307.0970 at 10iterations 6.405571 149.8124 at 20iterations 3.794984 83.07323 at 30iterations 2.239064 46.55197 at 40iterations 1.313391 25.45873 at 50iterations 0.7679540 15.33255 at 60iterations 0.4491239 9.364301 at 70iterations 0.2614773 5.175611 at 80iterations 0.1520458 3.319450 at 90iterations 8.8413551E-02 1.822145 at 100iterations 5.1311173E-02 0.9641743 at 110iterations 2.9799540E-02 0.5396574 at 120iterations 1.7295538E-02 0.3183203 at 130iterations 1.0007676E-02 0.1877651 at 140iterations 5.8035729E-03 0.1025677 at 150iterations 3.3615478E-03 5.2316666E-02 at 160iterations 1.9448614E-03 3.4365177E-02 at 170iterations 1.1266719E-03 1.9142151E-02 at 180iterations finished qdiffx linear iterations at : 21:07:35 total time elapsed so far: 19.84000 # loops : 180 mean,max change (kT/e) : 1.1266719E-03 1.9142151E-02 energy calculations done at 19.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.01000 DelPhi exited at 21:07:35 20.018u 0.486s 0:20.98 97.6% 0+0k 0+0io 0pf+0w