Mon Oct 10 13:55:39 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 Mon Oct 10 2011 at 13:55:39 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3333 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: 0.5683451 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): -54.70800 2.177000 ymin,ymax (A): -18.51700 44.12100 zmin,zma (A): -67.14000 -13.12200 x,y,z range (A): 56.88500 62.63800 54.01800 scale (grids/A): 0.5683451 object centre (A): -26.26550 12.80200 -40.13100 number of atom coordinates read : 3333 total number of charged atoms : 3184 net assigned charge : 5.500012 assigned positive charge : 505.6205 centred at (gu) : 89.83067 89.85800 89.46990 assigned negative charge : -500.1218 centred at (gu) : 89.92661 89.84708 89.45166 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7330 nv = 96 ne = 84 npr = 64429 no. pairs analyzed = 64429 no. exposed pairs = 4500 no. arc points = 33328 no. surface atoms = 1479 nbur = 1854 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 = 1.512000 m= 337 mr = 3572 m= 0 mr = 29 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 4066 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3425 ## 413 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9364 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5116184E-10 9.7087705E-10 midg,1,midg; midg,igrid,midg 6.3221911E-10 9.4511565E-10 1,midg,midg; igrid,midg,midg 2.4774942E-09 -7.9215301E-10 gauss-seidel spectral radius is 0.9840701 estimated iterations to convergence 65 setup time was (sec) 0.4300000 now iterating at: 13:55:40 rms-change max change #iterations 9.5950544E-02 16.27890 at 10iterations 7.0106937E-03 1.069077 at 20iterations 5.2894052E-04 7.7755928E-02 at 30iterations 3.8758375E-05 6.0176849E-03 at 40iterations 2.9627427E-06 4.3964386E-04 at 50iterations finished qdiffx linear iterations at : 13:55:43 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 2.9627427E-06 4.3964386E-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) 3.480000 DelPhi exited at 13:55:44 3.479u 0.205s 0:04.42 83.0% 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 Mon Oct 10 2011 at 13:55:44 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 = 3333 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: 1.705035 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): -54.70800 2.177000 ymin,ymax (A): -18.51700 44.12100 zmin,zma (A): -67.14000 -13.12200 x,y,z range (A): 56.88500 62.63800 54.01800 scale (grids/A): 1.705035 object centre (A): -26.26550 12.80200 -40.13100 number of atom coordinates read : 3333 total number of charged atoms : 3184 net assigned charge : 5.500012 assigned positive charge : 505.6205 centred at (gu) : 89.49111 89.57307 88.40882 assigned negative charge : -500.1218 centred at (gu) : 89.77948 89.54073 88.35442 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80226 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33328 grid for indexing accessible points = 1.400000 m= 25059 mr = 52807 m= 2986 mr = 16718 m= 130 mr = 1475 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1832 time to turn everything in is 0.4000000 number of dielectric boundary points 37385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 353 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 24624 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) : 0.5683451 object centre at (A) : -26.26550 12.80200 -40.13100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4029318E-02 1.3822879E-02 midg,1,midg; midg,igrid,midg -1.4360657E-02 2.6595622E-02 1,midg,midg; igrid,midg,midg 3.9941827E-03 2.2314091E-03 gauss-seidel spectral radius is 0.9984047 estimated iterations to convergence 199 setup time was (sec) 0.6200000 now iterating at: 13:55:45 rms-change max change #iterations 3.901935 152.4401 at 10iterations 1.707766 57.55093 at 20iterations 0.7512775 23.77002 at 30iterations 0.3306284 10.42154 at 40iterations 0.1450768 4.735641 at 50iterations 6.3836105E-02 2.038397 at 60iterations 2.8072886E-02 0.9539871 at 70iterations 1.2356239E-02 0.4257889 at 80iterations 5.4162899E-03 0.1772537 at 90iterations 2.3929798E-03 7.5866699E-02 at 100iterations 1.0521685E-03 3.7288666E-02 at 110iterations 4.6425906E-04 1.6242981E-02 at 120iterations finished qdiffx linear iterations at : 13:55:52 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 4.6425906E-04 1.6242981E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 13:55:53 7.998u 0.229s 0:08.73 94.0% 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 Mon Oct 10 2011 at 13:55:53 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 = 3333 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: 2.557553 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): -54.70800 2.177000 ymin,ymax (A): -18.51700 44.12100 zmin,zma (A): -67.14000 -13.12200 x,y,z range (A): 56.88500 62.63800 54.01800 scale (grids/A): 2.557553 object centre (A): -26.26550 12.80200 -40.13100 number of atom coordinates read : 3333 total number of charged atoms : 3184 net assigned charge : 5.500012 assigned positive charge : 505.6205 centred at (gu) : 89.23631 89.35941 87.61288 assigned negative charge : -500.1218 centred at (gu) : 89.66909 89.31101 87.53149 start vw surface at 0.1200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 185778 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33328 grid for indexing accessible points = 1.400000 m= 85576 mr = 129441 m= 25390 mr = 66379 m= 4809 mr = 18432 m= 443 mr = 3142 m= 7 mr = 252 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 6305 time to turn everything in is 0.9800000 number of dielectric boundary points 84357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 25457 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) : 1.705035 object centre at (A) : -26.26550 12.80200 -40.13100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2328455 0.2382751 midg,1,midg; midg,igrid,midg -0.4661003 0.4019541 1,midg,midg; igrid,midg,midg 2.8410016E-02 1.9037828E-02 gauss-seidel spectral radius is 0.9992266 estimated iterations to convergence 284 setup time was (sec) 1.220000 now iterating at: 13:55:54 rms-change max change #iterations 9.913749 285.9204 at 10iterations 5.809848 203.9611 at 20iterations 3.384398 86.10172 at 30iterations 1.957163 42.27905 at 40iterations 1.126335 25.89435 at 50iterations 0.6467439 15.65075 at 60iterations 0.3704723 7.403955 at 70iterations 0.2117362 3.964600 at 80iterations 0.1209568 2.230006 at 90iterations 6.8991549E-02 1.276584 at 100iterations 3.9206769E-02 0.8171291 at 110iterations 2.2316674E-02 0.4068794 at 120iterations 1.2693717E-02 0.2407379 at 130iterations 7.2038402E-03 0.1326556 at 140iterations 4.1059875E-03 9.1240525E-02 at 150iterations 2.3280042E-03 4.4342041E-02 at 160iterations 1.3246144E-03 2.5695801E-02 at 170iterations 7.5162912E-04 1.4886856E-02 at 180iterations finished qdiffx linear iterations at : 13:56:06 total time elapsed so far: 13.18000 # loops : 180 mean,max change (kT/e) : 7.5162912E-04 1.4886856E-02 energy calculations done at 13.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 13:56:07 13.327u 0.284s 0:14.04 96.8% 0+0k 0+0io 0pf+0w