Sat Oct 8 13:46:39 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+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 Sat Oct 8 2011 at 13:46:39 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2945 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 0.6316648 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): -11.39000 43.34700 ymin,ymax (A): 10.92000 55.41700 zmin,zma (A): 37.88300 94.24200 x,y,z range (A): 54.73700 44.49700 56.35900 scale (grids/A): 0.6316648 object centre (A): 15.97850 33.16850 66.06250 number of atom coordinates read : 2945 total number of charged atoms : 2798 net assigned charge : -2.999993 assigned positive charge : 440.2137 centred at (gu) : 89.06773 89.39545 90.97512 assigned negative charge : -443.2144 centred at (gu) : 89.02316 89.30431 90.93423 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7884 nv = 96 ne = 84 npr = 60997 no. pairs analyzed = 60997 no. exposed pairs = 3430 no. arc points = 23350 no. surface atoms = 1168 nbur = 1777 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 4679 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2269 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9560 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2356706E-09 1.2327083E-09 midg,1,midg; midg,igrid,midg -1.4917656E-08 5.3920193E-09 1,midg,midg; igrid,midg,midg -9.8888675E-09 1.0589951E-09 gauss-seidel spectral radius is 0.9870431 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 13:46:39 rms-change max change #iterations 0.1509058 21.96829 at 10iterations 1.5057699E-02 2.406828 at 20iterations 1.6475719E-03 0.2485275 at 30iterations 2.5692765E-04 3.9604187E-02 at 40iterations 5.8434434E-05 9.8190308E-03 at 50iterations finished qdiffx linear iterations at : 13:46:42 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 5.8434434E-05 9.8190308E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 13:46:42 3.205u 0.176s 0:03.68 91.5% 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 Sat Oct 8 2011 at 13:46:42 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2945 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 1.894994 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): -11.39000 43.34700 ymin,ymax (A): 10.92000 55.41700 zmin,zma (A): 37.88300 94.24200 x,y,z range (A): 54.73700 44.49700 56.35900 scale (grids/A): 1.894994 object centre (A): 15.97850 33.16850 66.06250 number of atom coordinates read : 2945 total number of charged atoms : 2798 net assigned charge : -2.999993 assigned positive charge : 440.2137 centred at (gu) : 87.20265 88.18570 92.92480 assigned negative charge : -443.2144 centred at (gu) : 87.06925 87.91255 92.80251 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 86395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23350 grid for indexing accessible points = 1.400000 m= 32291 mr = 62929 m= 4977 mr = 24672 m= 277 mr = 3129 m= 2 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 33119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 21960 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) : 0.6316648 object centre at (A) : 15.97850 33.16850 66.06250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7684210E-02 6.8619801E-03 midg,1,midg; midg,igrid,midg -5.3156740E-03 1.1015691E-02 1,midg,midg; igrid,midg,midg -5.8842544E-02 -2.4843065E-03 gauss-seidel spectral radius is 0.9986514 estimated iterations to convergence 216 setup time was (sec) 0.8900000 now iterating at: 13:46:43 rms-change max change #iterations 4.566579 175.5628 at 10iterations 2.158162 70.33890 at 20iterations 1.018164 31.53355 at 30iterations 0.4791311 13.86264 at 40iterations 0.2254604 6.560295 at 50iterations 0.1066246 3.140366 at 60iterations 5.0076310E-02 1.453767 at 70iterations 2.3743400E-02 0.7576079 at 80iterations 1.1212301E-02 0.3329592 at 90iterations 5.3079771E-03 0.1712909 at 100iterations 2.5090869E-03 7.3677063E-02 at 110iterations 1.1984725E-03 3.5524368E-02 at 120iterations finished qdiffx linear iterations at : 13:46:50 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 1.1984725E-03 3.5524368E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 13:46:50 7.463u 0.196s 0:07.95 96.2% 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 Sat Oct 8 2011 at 13:46:50 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2945 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 2.842492 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): -11.39000 43.34700 ymin,ymax (A): 10.92000 55.41700 zmin,zma (A): 37.88300 94.24200 x,y,z range (A): 54.73700 44.49700 56.35900 scale (grids/A): 2.842492 object centre (A): 15.97850 33.16850 66.06250 number of atom coordinates read : 2945 total number of charged atoms : 2798 net assigned charge : -2.999993 assigned positive charge : 440.2137 centred at (gu) : 85.80392 87.27850 94.38689 assigned negative charge : -443.2144 centred at (gu) : 85.60390 86.86895 94.20367 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 199893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23350 grid for indexing accessible points = 1.400000 m= 105538 mr = 151691 m= 38211 mr = 88526 m= 8777 mr = 31354 m= 1192 mr = 6578 m= 51 mr = 782 m= 0 mr = 13 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.530000 number of dielectric boundary points 74718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 22381 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) : 1.894994 object centre at (A) : 15.97850 33.16850 66.06250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0435147E-02 0.1613519 midg,1,midg; midg,igrid,midg -3.2040890E-02 0.1352041 1,midg,midg; igrid,midg,midg -0.8183678 0.1733250 gauss-seidel spectral radius is 0.9992648 estimated iterations to convergence 291 setup time was (sec) 1.850000 now iterating at: 13:46:52 rms-change max change #iterations 10.65552 296.6078 at 10iterations 6.268740 157.7863 at 20iterations 3.649063 71.89247 at 30iterations 2.125692 41.37406 at 40iterations 1.232377 23.97221 at 50iterations 0.7132325 14.04258 at 60iterations 0.4137757 8.319927 at 70iterations 0.2390507 4.378967 at 80iterations 0.1379413 2.289558 at 90iterations 7.9717629E-02 1.295466 at 100iterations 4.6002183E-02 0.9547031 at 110iterations 2.6573677E-02 0.4340248 at 120iterations 1.5324832E-02 0.2459087 at 130iterations 8.8744853E-03 0.1488609 at 140iterations 5.1348223E-03 8.0873728E-02 at 150iterations 2.9823829E-03 5.2276611E-02 at 160iterations 1.7432821E-03 3.2176018E-02 at 170iterations 1.0270985E-03 1.7324448E-02 at 180iterations finished qdiffx linear iterations at : 13:47:04 total time elapsed so far: 13.55000 # loops : 180 mean,max change (kT/e) : 1.0270985E-03 1.7324448E-02 energy calculations done at 13.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.74000 DelPhi exited at 13:47:05 13.738u 0.204s 0:14.22 97.9% 0+0k 0+0io 0pf+0w