Sun Oct 9 08:36:26 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 Sun Oct 9 2011 at 08:36:26 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 = 6140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4767836 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): -15.07900 51.91400 ymin,ymax (A): -16.61100 49.62400 zmin,zma (A): -6.363000 68.30400 x,y,z range (A): 66.99300 66.23500 74.66700 scale (grids/A): 0.4767836 object centre (A): 18.41750 16.50650 30.97050 number of atom coordinates read : 6140 total number of charged atoms : 5971 net assigned charge : -3.999988 assigned positive charge : 924.6512 centred at (gu) : 89.88193 90.45901 90.67289 assigned negative charge : -928.6596 centred at (gu) : 89.95284 90.40025 90.75166 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8648 nv = 96 ne = 84 npr = 122940 no. pairs analyzed = 122940 no. exposed pairs = 7714 no. arc points = 53676 no. surface atoms = 2560 nbur = 3580 mkacc time = 0.2100000 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 = 1.792000 m= 282 mr = 4352 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3900000 number of dielectric boundary points 4575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5015 ## 896 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 11807 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6907106E-11 -8.2686052E-11 midg,1,midg; midg,igrid,midg -4.7129620E-11 3.5042393E-11 1,midg,midg; igrid,midg,midg 4.0600464E-11 -6.0473446E-11 gauss-seidel spectral radius is 0.9776166 estimated iterations to convergence 55 setup time was (sec) 0.5800000 now iterating at: 08:36:27 rms-change max change #iterations 5.4706775E-02 9.543579 at 10iterations 2.9388308E-03 0.5042572 at 20iterations 4.4310346E-04 0.1146412 at 30iterations 1.2746907E-04 3.2264709E-02 at 40iterations 3.9690978E-05 9.5939636E-03 at 50iterations finished qdiffx linear iterations at : 08:36:30 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 3.9690978E-05 9.5939636E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 08:36:30 3.629u 0.182s 0:04.13 92.0% 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 Sun Oct 9 2011 at 08:36:30 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 = 6140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.430351 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): -15.07900 51.91400 ymin,ymax (A): -16.61100 49.62400 zmin,zma (A): -6.363000 68.30400 x,y,z range (A): 66.99300 66.23500 74.66700 scale (grids/A): 1.430351 object centre (A): 18.41750 16.50650 30.97050 number of atom coordinates read : 6140 total number of charged atoms : 5971 net assigned charge : -3.999988 assigned positive charge : 924.6512 centred at (gu) : 89.64367 91.37477 92.01704 assigned negative charge : -928.6596 centred at (gu) : 89.85820 91.20049 92.25455 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 99964 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53676 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 26140 mr = 68043 m= 1754 mr = 16432 m= 22 mr = 544 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 261 time to turn everything in is 0.4800000 number of dielectric boundary points 42861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 866 ## 19 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 43693 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) : 0.4767836 object centre at (A) : 18.41750 16.50650 30.97050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7818731E-03 -3.1395901E-02 midg,1,midg; midg,igrid,midg -8.7159770E-03 2.5740836E-03 1,midg,midg; igrid,midg,midg 1.2331774E-02 -3.1158931E-04 gauss-seidel spectral radius is 0.9979278 estimated iterations to convergence 175 setup time was (sec) 0.7100000 now iterating at: 08:36:31 rms-change max change #iterations 3.728821 135.5108 at 10iterations 1.464161 47.19503 at 20iterations 0.5747616 18.43035 at 30iterations 0.2265709 7.679306 at 40iterations 8.9356504E-02 2.928329 at 50iterations 3.5214152E-02 1.160646 at 60iterations 1.3941205E-02 0.3934174 at 70iterations 5.5559315E-03 0.1862583 at 80iterations 2.2536218E-03 8.3210945E-02 at 90iterations 9.5203612E-04 3.4828663E-02 at 100iterations 4.3456160E-04 1.9134521E-02 at 110iterations 2.2492433E-04 9.6969604E-03 at 120iterations finished qdiffx linear iterations at : 08:36:38 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 2.2492433E-04 9.6969604E-03 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 08:36:39 7.947u 0.221s 0:08.43 96.7% 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 08:36:39 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 = 6140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.145526 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): -15.07900 51.91400 ymin,ymax (A): -16.61100 49.62400 zmin,zma (A): -6.363000 68.30400 x,y,z range (A): 66.99300 66.23500 74.66700 scale (grids/A): 2.145526 object centre (A): 18.41750 16.50650 30.97050 number of atom coordinates read : 6140 total number of charged atoms : 5971 net assigned charge : -3.999988 assigned positive charge : 924.6512 centred at (gu) : 89.46501 92.06171 93.02527 assigned negative charge : -928.6596 centred at (gu) : 89.78709 91.80061 93.38168 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 233794 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53676 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 98464 mr = 168438 m= 20928 mr = 74969 m= 2193 mr = 14104 m= 63 mr = 1096 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 772 time to turn everything in is 1.190000 number of dielectric boundary points 96836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 47489 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) : 1.430351 object centre at (A) : 18.41750 16.50650 30.97050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1995798 -0.8861236 midg,1,midg; midg,igrid,midg -0.1799273 9.3245298E-02 1,midg,midg; igrid,midg,midg 0.3107939 1.7572964E-02 gauss-seidel spectral radius is 0.9991414 estimated iterations to convergence 270 setup time was (sec) 1.490000 now iterating at: 08:36:40 rms-change max change #iterations 10.69394 283.1423 at 10iterations 6.132400 133.6107 at 20iterations 3.493067 71.89822 at 30iterations 1.974009 50.77409 at 40iterations 1.114215 23.19431 at 50iterations 0.6256744 12.40092 at 60iterations 0.3504155 6.931614 at 70iterations 0.1957690 3.611832 at 80iterations 0.1092580 2.430603 at 90iterations 6.0702950E-02 1.131613 at 100iterations 3.3882555E-02 0.6951756 at 110iterations 1.8796096E-02 0.3712711 at 120iterations 1.0442602E-02 0.1914470 at 130iterations 5.7841595E-03 0.1266143 at 140iterations 3.2188473E-03 6.1467677E-02 at 150iterations 1.7908261E-03 3.6996841E-02 at 160iterations 9.9869294E-04 2.4535179E-02 at 170iterations 5.6094257E-04 1.1013985E-02 at 180iterations finished qdiffx linear iterations at : 08:36:54 total time elapsed so far: 14.67000 # loops : 180 mean,max change (kT/e) : 5.6094257E-04 1.1013985E-02 energy calculations done at 14.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.80000 DelPhi exited at 08:36:54 14.800u 0.304s 0:15.43 97.8% 0+0k 0+0io 0pf+0w