Sun Oct 9 17:28:57 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 17:28:57 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5005 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5639872 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): 3.211000 64.99900 ymin,ymax (A): -8.642000 53.45100 zmin,zma (A): -1.167000 61.95500 x,y,z range (A): 61.78800 62.09300 63.12200 scale (grids/A): 0.5639872 object centre (A): 34.10500 22.40450 30.39400 number of atom coordinates read : 5005 total number of charged atoms : 4860 net assigned charge : 0.1350470 assigned positive charge : 771.3279 centred at (gu) : 88.34912 89.24884 89.15222 assigned negative charge : -771.1985 centred at (gu) : 88.24412 89.28468 89.12354 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 10453 nv = 96 ne = 84 npr = 101183 no. pairs analyzed = 101183 no. exposed pairs = 5941 no. arc points = 40017 no. surface atoms = 2023 nbur = 2982 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 = 1.540000 m= 487 mr = 6000 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 4917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4059 ## 425 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 13602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0707601E-10 5.6073612E-10 midg,1,midg; midg,igrid,midg 1.0165699E-09 -6.1028865E-10 1,midg,midg; igrid,midg,midg -3.4328644E-09 1.5711910E-09 gauss-seidel spectral radius is 0.9839317 estimated iterations to convergence 65 setup time was (sec) 0.7000000 now iterating at: 17:28:58 rms-change max change #iterations 0.1203360 15.11187 at 10iterations 1.0650327E-02 1.335777 at 20iterations 2.6910566E-03 0.3003235 at 30iterations 1.2329106E-03 0.1301193 at 40iterations 6.0166995E-04 6.6930771E-02 at 50iterations finished qdiffx linear iterations at : 17:29:00 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 6.0166995E-04 6.6930771E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 17:29:01 3.500u 0.233s 0:04.02 92.7% 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 17:29:01 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5005 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.691962 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): 3.211000 64.99900 ymin,ymax (A): -8.642000 53.45100 zmin,zma (A): -1.167000 61.95500 x,y,z range (A): 61.78800 62.09300 63.12200 scale (grids/A): 1.691962 object centre (A): 34.10500 22.40450 30.39400 number of atom coordinates read : 5005 total number of charged atoms : 4860 net assigned charge : 0.1350470 assigned positive charge : 771.3279 centred at (gu) : 85.04585 87.74515 87.45536 assigned negative charge : -771.1985 centred at (gu) : 84.73209 87.85412 87.37057 start vw surface at 0.2400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 116481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40017 grid for indexing accessible points = 1.400000 m= 41450 mr = 84523 m= 5301 mr = 30131 m= 177 mr = 2913 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 45815 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 350 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 37473 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) : 0.5639872 object centre at (A) : 34.10500 22.40450 30.39400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7683426E-02 -2.9990047E-02 midg,1,midg; midg,igrid,midg 1.9732906E-02 9.3108620E-03 1,midg,midg; igrid,midg,midg -2.0427540E-02 2.8775655E-02 gauss-seidel spectral radius is 0.9984984 estimated iterations to convergence 205 setup time was (sec) 1.070000 now iterating at: 17:29:02 rms-change max change #iterations 5.000975 211.1880 at 10iterations 2.252814 77.08957 at 20iterations 1.020177 30.46257 at 30iterations 0.4617501 12.84408 at 40iterations 0.2086702 5.699997 at 50iterations 9.5017761E-02 2.541935 at 60iterations 4.3298814E-02 1.237267 at 70iterations 2.0095300E-02 0.5932398 at 80iterations 9.7306520E-03 0.2797394 at 90iterations 5.1423302E-03 0.1365290 at 100iterations 3.0869441E-03 8.2984924E-02 at 110iterations 2.1120301E-03 5.1003635E-02 at 120iterations finished qdiffx linear iterations at : 17:29:08 total time elapsed so far: 7.140000 # loops : 120 mean,max change (kT/e) : 2.1120301E-03 5.1003635E-02 energy calculations done at 7.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.310000 DelPhi exited at 17:29:09 7.309u 0.176s 0:07.80 95.7% 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 17:29:09 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5005 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.537942 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): 3.211000 64.99900 ymin,ymax (A): -8.642000 53.45100 zmin,zma (A): -1.167000 61.95500 x,y,z range (A): 61.78800 62.09300 63.12200 scale (grids/A): 2.537942 object centre (A): 34.10500 22.40450 30.39400 number of atom coordinates read : 5005 total number of charged atoms : 4860 net assigned charge : 0.1350470 assigned positive charge : 771.3279 centred at (gu) : 82.56829 86.61727 86.18277 assigned negative charge : -771.1985 centred at (gu) : 82.09803 86.78108 86.05582 start vw surface at 0.2200000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 270470 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40017 grid for indexing accessible points = 1.400000 m= 138369 mr = 205231 m= 45336 mr = 113037 m= 8770 mr = 35482 m= 838 mr = 6106 m= 25 mr = 441 m= 0 mr = 2 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.910000 number of dielectric boundary points 103509 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 38852 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) : 1.691962 object centre at (A) : 34.10500 22.40450 30.39400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4218343 -0.7171710 midg,1,midg; midg,igrid,midg 3.9539821E-03 -7.0304917E-03 1,midg,midg; igrid,midg,midg -0.3952028 0.3261208 gauss-seidel spectral radius is 0.9992722 estimated iterations to convergence 293 setup time was (sec) 2.200000 now iterating at: 17:29:11 rms-change max change #iterations 12.57851 315.8185 at 10iterations 7.467500 160.1805 at 20iterations 4.403578 85.50323 at 30iterations 2.593531 44.89487 at 40iterations 1.517325 25.32210 at 50iterations 0.8869811 16.69495 at 60iterations 0.5168654 8.231840 at 70iterations 0.3011559 4.895016 at 80iterations 0.1751117 2.901727 at 90iterations 0.1017522 1.639502 at 100iterations 5.9147734E-02 0.9671478 at 110iterations 3.4507804E-02 0.5613480 at 120iterations 2.0246871E-02 0.3229780 at 130iterations 1.2060107E-02 0.1963654 at 140iterations 7.3906183E-03 0.1227283 at 150iterations 4.7450946E-03 8.0815315E-02 at 160iterations 3.2615366E-03 5.3554535E-02 at 170iterations 2.4186110E-03 3.8333893E-02 at 180iterations finished qdiffx linear iterations at : 17:29:21 total time elapsed so far: 12.00000 # loops : 180 mean,max change (kT/e) : 2.4186110E-03 3.8333893E-02 energy calculations done at 12.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 17:29:22 12.185u 0.177s 0:12.64 97.7% 0+0k 0+0io 0pf+0w