Tue Oct 11 03:48:40 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 03:48:40 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2735 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 0.6639561 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): -10.99700 36.95000 ymin,ymax (A): -26.58900 23.28100 zmin,zma (A): -8.422999 45.19500 x,y,z range (A): 47.94700 49.87000 53.61800 scale (grids/A): 0.6639561 object centre (A): 12.97650 -1.653999 18.38600 number of atom coordinates read : 2735 total number of charged atoms : 2605 net assigned charge : 3.926018 assigned positive charge : 422.2687 centred at (gu) : 89.98595 89.96262 91.39697 assigned negative charge : -418.3432 centred at (gu) : 89.75225 89.80722 91.44006 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8053 nv = 96 ne = 84 npr = 55114 no. pairs analyzed = 55114 no. exposed pairs = 3443 no. arc points = 23458 no. surface atoms = 1144 nbur = 1591 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4484 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3600000 number of dielectric boundary points 3958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2230 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9528 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6159388E-08 1.3374883E-09 midg,1,midg; midg,igrid,midg -2.6036172E-08 4.6997933E-08 1,midg,midg; igrid,midg,midg -4.5171443E-08 6.4868054E-08 gauss-seidel spectral radius is 0.9882519 estimated iterations to convergence 75 setup time was (sec) 0.6300000 now iterating at: 03:48:41 rms-change max change #iterations 0.1769181 26.45851 at 10iterations 1.9240376E-02 2.717854 at 20iterations 2.1457647E-03 0.2774973 at 30iterations 2.5297227E-04 3.6254883E-02 at 40iterations 3.7706548E-05 5.3710938E-03 at 50iterations finished qdiffx linear iterations at : 03:48:44 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 3.7706548E-05 5.3710938E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 03:48:45 4.218u 0.242s 0:04.83 92.1% 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 Tue Oct 11 2011 at 03:48:45 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2735 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 1.991868 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): -10.99700 36.95000 ymin,ymax (A): -26.58900 23.28100 zmin,zma (A): -8.422999 45.19500 x,y,z range (A): 47.94700 49.87000 53.61800 scale (grids/A): 1.991868 object centre (A): 12.97650 -1.653999 18.38600 number of atom coordinates read : 2735 total number of charged atoms : 2605 net assigned charge : 3.926018 assigned positive charge : 422.2687 centred at (gu) : 89.95739 89.88714 94.19035 assigned negative charge : -418.3432 centred at (gu) : 89.25633 89.42123 94.31960 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 85630 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23458 grid for indexing accessible points = 1.400000 m= 32496 mr = 59872 m= 5858 mr = 24177 m= 448 mr = 3823 m= 6 mr = 185 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1136 time to turn everything in is 0.7200000 number of dielectric boundary points 36381 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20595 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) : 0.6639561 object centre at (A) : 12.97650 -1.653999 18.38600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4121413E-02 1.1184546E-02 midg,1,midg; midg,igrid,midg -2.7117692E-02 5.6631207E-03 1,midg,midg; igrid,midg,midg -1.1504339E-02 7.2863787E-02 gauss-seidel spectral radius is 0.9987614 estimated iterations to convergence 225 setup time was (sec) 1.050000 now iterating at: 03:48:46 rms-change max change #iterations 4.905997 238.0749 at 10iterations 2.387754 78.49564 at 20iterations 1.161147 37.68715 at 30iterations 0.5643377 18.21608 at 40iterations 0.2746613 7.922722 at 50iterations 0.1332059 3.777822 at 60iterations 6.4965285E-02 1.969068 at 70iterations 3.1635836E-02 0.9168482 at 80iterations 1.5336368E-02 0.4430847 at 90iterations 7.4508372E-03 0.2045002 at 100iterations 3.6247878E-03 0.1064677 at 110iterations 1.7652492E-03 4.9480438E-02 at 120iterations finished qdiffx linear iterations at : 03:48:54 total time elapsed so far: 9.520000 # loops : 120 mean,max change (kT/e) : 1.7652492E-03 4.9480438E-02 energy calculations done at 9.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.700000 DelPhi exited at 03:48:55 9.708u 0.268s 0:10.39 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 Tue Oct 11 2011 at 03:48:55 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2735 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 2.987803 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): -10.99700 36.95000 ymin,ymax (A): -26.58900 23.28100 zmin,zma (A): -8.422999 45.19500 x,y,z range (A): 47.94700 49.87000 53.61800 scale (grids/A): 2.987803 object centre (A): 12.97650 -1.653999 18.38600 number of atom coordinates read : 2735 total number of charged atoms : 2605 net assigned charge : 3.926018 assigned positive charge : 422.2687 centred at (gu) : 89.93597 89.83054 96.28548 assigned negative charge : -418.3432 centred at (gu) : 88.88451 89.13174 96.47939 start vw surface at 0.1600000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 197963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23458 grid for indexing accessible points = 1.400000 m= 102970 mr = 144939 m= 39973 mr = 84533 m= 10814 mr = 32666 m= 1901 mr = 8301 m= 147 mr = 1338 m= 3 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 3985 time to turn everything in is 1.810000 number of dielectric boundary points 81916 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 20840 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) : 1.991868 object centre at (A) : 12.97650 -1.653999 18.38600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1943032 0.3038372 midg,1,midg; midg,igrid,midg -0.2674322 -7.1598478E-02 1,midg,midg; igrid,midg,midg -3.3254184E-02 0.6303329 gauss-seidel spectral radius is 0.9992906 estimated iterations to convergence 296 setup time was (sec) 2.140000 now iterating at: 03:48:57 rms-change max change #iterations 11.06784 363.9941 at 10iterations 6.501751 165.1530 at 20iterations 3.813596 99.42551 at 30iterations 2.235425 41.76961 at 40iterations 1.311042 23.90276 at 50iterations 0.7666864 14.65646 at 60iterations 0.4469275 7.378384 at 70iterations 0.2610271 4.412651 at 80iterations 0.1524290 2.692582 at 90iterations 8.8686109E-02 1.526443 at 100iterations 5.1813331E-02 0.8204689 at 110iterations 3.0186431E-02 0.4773254 at 120iterations 1.7616943E-02 0.2832947 at 130iterations 1.0273597E-02 0.1697788 at 140iterations 6.0107447E-03 0.1009979 at 150iterations 3.5256089E-03 6.1105967E-02 at 160iterations 2.0742291E-03 3.3535004E-02 at 170iterations 1.2328518E-03 2.3334503E-02 at 180iterations finished qdiffx linear iterations at : 03:49:11 total time elapsed so far: 15.72000 # loops : 180 mean,max change (kT/e) : 1.2328518E-03 2.3334503E-02 energy calculations done at 15.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.90000 DelPhi exited at 03:49:12 15.901u 0.295s 0:16.65 97.2% 0+0k 0+0io 0pf+0w