Mon Oct 10 22:34:42 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 22:34:42 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2630 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6722181 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): -19.60100 30.83100 ymin,ymax (A): 20.10200 73.06100 zmin,zma (A): 9.254001 51.86400 x,y,z range (A): 50.43200 52.95900 42.61000 scale (grids/A): 0.6722181 object centre (A): 5.615000 46.58150 30.55900 number of atom coordinates read : 2630 total number of charged atoms : 2489 net assigned charge : 6.500023 assigned positive charge : 396.1898 centred at (gu) : 91.48862 89.35100 89.83336 assigned negative charge : -389.6904 centred at (gu) : 91.48497 89.64049 90.05239 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7854 nv = 96 ne = 84 npr = 53952 no. pairs analyzed = 53952 no. exposed pairs = 3038 no. arc points = 21104 no. surface atoms = 1026 nbur = 1604 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 467 mr = 4574 m= 0 mr = 69 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 179 time to turn everything in is 0.3400000 number of dielectric boundary points 3678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1857 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9103 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2816996E-08 -3.6767887E-08 midg,1,midg; midg,igrid,midg 1.1212265E-07 -5.0632703E-08 1,midg,midg; igrid,midg,midg 1.5960469E-08 3.1326149E-08 gauss-seidel spectral radius is 0.9885265 estimated iterations to convergence 76 setup time was (sec) 0.6000000 now iterating at: 22:34:43 rms-change max change #iterations 0.1863333 25.11416 at 10iterations 2.1119483E-02 2.751343 at 20iterations 2.8418645E-03 0.5184021 at 30iterations 6.2086899E-04 0.1262398 at 40iterations 2.0660991E-04 4.3380737E-02 at 50iterations finished qdiffx linear iterations at : 22:34:46 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 2.0660991E-04 4.3380737E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 22:34:46 3.601u 0.168s 0:04.07 92.3% 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 22:34:46 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2630 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.016654 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): -19.60100 30.83100 ymin,ymax (A): 20.10200 73.06100 zmin,zma (A): 9.254001 51.86400 x,y,z range (A): 50.43200 52.95900 42.61000 scale (grids/A): 2.016654 object centre (A): 5.615000 46.58150 30.55900 number of atom coordinates read : 2630 total number of charged atoms : 2489 net assigned charge : 6.500023 assigned positive charge : 396.1898 centred at (gu) : 94.46519 88.05222 89.49961 assigned negative charge : -389.6904 centred at (gu) : 94.45454 88.92102 90.15685 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 84741 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21104 grid for indexing accessible points = 1.400000 m= 31814 mr = 60306 m= 5682 mr = 24364 m= 417 mr = 3957 m= 8 mr = 227 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 4359 time to turn everything in is 0.6500000 number of dielectric boundary points 33808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19683 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) : 0.6722181 object centre at (A) : 5.615000 46.58150 30.55900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7796888E-02 3.6033418E-03 midg,1,midg; midg,igrid,midg 2.2091074E-02 -3.7430018E-02 1,midg,midg; igrid,midg,midg 2.0267578E-02 1.6972438E-03 gauss-seidel spectral radius is 0.9987713 estimated iterations to convergence 226 setup time was (sec) 0.9400000 now iterating at: 22:34:48 rms-change max change #iterations 4.764708 186.3030 at 10iterations 2.318776 74.77030 at 20iterations 1.130512 33.98331 at 30iterations 0.5496902 15.99248 at 40iterations 0.2682674 7.681782 at 50iterations 0.1310413 3.830657 at 60iterations 6.3772835E-02 1.870075 at 70iterations 3.1384956E-02 0.8746796 at 80iterations 1.5411019E-02 0.4324722 at 90iterations 7.6445057E-03 0.2190514 at 100iterations 3.8625153E-03 0.1280441 at 110iterations 2.0312977E-03 6.7771912E-02 at 120iterations finished qdiffx linear iterations at : 22:34:55 total time elapsed so far: 8.520000 # loops : 120 mean,max change (kT/e) : 2.0312977E-03 6.7771912E-02 energy calculations done at 8.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.720000 DelPhi exited at 22:34:56 8.718u 0.229s 0:09.49 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 22:34:56 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2630 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: 3.024981 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): -19.60100 30.83100 ymin,ymax (A): 20.10200 73.06100 zmin,zma (A): 9.254001 51.86400 x,y,z range (A): 50.43200 52.95900 42.61000 scale (grids/A): 3.024981 object centre (A): 5.615000 46.58150 30.55900 number of atom coordinates read : 2630 total number of charged atoms : 2489 net assigned charge : 6.500023 assigned positive charge : 396.1898 centred at (gu) : 96.69759 87.07814 89.24934 assigned negative charge : -389.6904 centred at (gu) : 96.68179 88.38150 90.23515 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 195885 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21104 grid for indexing accessible points = 1.400000 m= 101496 mr = 145376 m= 39049 mr = 84712 m= 10512 mr = 32528 m= 1882 mr = 8514 m= 197 mr = 1428 m= 7 mr = 139 m= 0 mr = 5 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 14566 time to turn everything in is 1.630000 number of dielectric boundary points 76326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 19912 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) : 2.016654 object centre at (A) : 5.615000 46.58150 30.55900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5040469 0.1048385 midg,1,midg; midg,igrid,midg -0.2514381 -0.3076612 1,midg,midg; igrid,midg,midg 0.1203781 5.7161752E-02 gauss-seidel spectral radius is 0.9992875 estimated iterations to convergence 296 setup time was (sec) 1.940000 now iterating at: 22:34:58 rms-change max change #iterations 10.79592 396.8087 at 10iterations 6.312998 142.8563 at 20iterations 3.687316 71.87969 at 30iterations 2.152139 36.87591 at 40iterations 1.253375 22.57487 at 50iterations 0.7290290 12.68231 at 60iterations 0.4244375 7.026815 at 70iterations 0.2469070 4.072430 at 80iterations 0.1433842 2.765125 at 90iterations 8.3628967E-02 1.441631 at 100iterations 4.8655007E-02 0.8782320 at 110iterations 2.8338958E-02 0.5156708 at 120iterations 1.6556747E-02 0.2904358 at 130iterations 9.7638750E-03 0.1692543 at 140iterations 5.8086123E-03 0.1114545 at 150iterations 3.5415050E-03 7.0247650E-02 at 160iterations 2.2491280E-03 4.8179626E-02 at 170iterations 1.5110362E-03 3.6739349E-02 at 180iterations finished qdiffx linear iterations at : 22:35:09 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 1.5110362E-03 3.6739349E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 22:35:10 13.151u 0.241s 0:13.98 95.7% 0+0k 0+0io 0pf+0w