Sat Oct 8 13:47:13 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 Sat Oct 8 2011 at 13:47:13 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 = 2972 !!! 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: 0.6276113 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): -11.36500 43.25800 ymin,ymax (A): 10.88000 54.99200 zmin,zma (A): 36.86500 93.58801 x,y,z range (A): 54.62300 44.11200 56.72300 scale (grids/A): 0.6276113 object centre (A): 15.94650 32.93600 65.22650 number of atom coordinates read : 2972 total number of charged atoms : 2825 net assigned charge : -1.999992 assigned positive charge : 445.0956 centred at (gu) : 89.10397 89.57700 91.20786 assigned negative charge : -447.0964 centred at (gu) : 89.07811 89.48868 91.12717 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7806 nv = 96 ne = 84 npr = 62256 no. pairs analyzed = 62256 no. exposed pairs = 3396 no. arc points = 23321 no. surface atoms = 1152 nbur = 1820 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 395 mr = 4599 m= 0 mr = 41 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3561 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2289 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9517 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.5227575E-09 7.3052786E-09 midg,1,midg; midg,igrid,midg -1.1560598E-08 5.6901492E-09 1,midg,midg; igrid,midg,midg -5.4940803E-09 3.0876127E-10 gauss-seidel spectral radius is 0.9868771 estimated iterations to convergence 71 setup time was (sec) 0.6500000 now iterating at: 13:47:14 rms-change max change #iterations 0.1465243 17.83706 at 10iterations 1.4271761E-02 2.116650 at 20iterations 1.5096853E-03 0.2634964 at 30iterations 2.1713755E-04 3.4004211E-02 at 40iterations 4.6932841E-05 8.1634521E-03 at 50iterations finished qdiffx linear iterations at : 13:47:17 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 4.6932841E-05 8.1634521E-03 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 13:47:18 4.100u 0.258s 0:04.66 93.3% 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 Sat Oct 8 2011 at 13:47:18 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 = 2972 !!! 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: 1.882834 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): -11.36500 43.25800 ymin,ymax (A): 10.88000 54.99200 zmin,zma (A): 36.86500 93.58801 x,y,z range (A): 54.62300 44.11200 56.72300 scale (grids/A): 1.882834 object centre (A): 15.94650 32.93600 65.22650 number of atom coordinates read : 2972 total number of charged atoms : 2825 net assigned charge : -1.999992 assigned positive charge : 445.0956 centred at (gu) : 87.31158 88.73042 93.62267 assigned negative charge : -447.0964 centred at (gu) : 87.23412 88.46566 93.38114 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 85546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23321 grid for indexing accessible points = 1.400000 m= 31400 mr = 62377 m= 4534 mr = 23833 m= 193 mr = 2744 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 481 time to turn everything in is 0.7300000 number of dielectric boundary points 32662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 22197 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) : 0.6276113 object centre at (A) : 15.94650 32.93600 65.22650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8916540E-02 1.5282561E-02 midg,1,midg; midg,igrid,midg -6.7698113E-03 9.9046743E-03 1,midg,midg; igrid,midg,midg -5.0592251E-02 4.7514816E-03 gauss-seidel spectral radius is 0.9986339 estimated iterations to convergence 214 setup time was (sec) 1.040000 now iterating at: 13:47:19 rms-change max change #iterations 4.513410 165.6967 at 10iterations 2.111812 70.25759 at 20iterations 0.9909360 29.84873 at 30iterations 0.4627816 16.48579 at 40iterations 0.2178215 7.888527 at 50iterations 0.1020674 2.879878 at 60iterations 4.8030350E-02 1.518727 at 70iterations 2.2501113E-02 0.7017241 at 80iterations 1.0638527E-02 0.3312826 at 90iterations 4.9971128E-03 0.1489182 at 100iterations 2.3579448E-03 7.8775406E-02 at 110iterations 1.1147454E-03 3.2658577E-02 at 120iterations finished qdiffx linear iterations at : 13:47:27 total time elapsed so far: 9.330000 # loops : 120 mean,max change (kT/e) : 1.1147454E-03 3.2658577E-02 energy calculations done at 9.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.510000 DelPhi exited at 13:47:28 9.510u 0.296s 0:10.09 97.1% 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 Sat Oct 8 2011 at 13:47:28 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 = 2972 !!! 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: 2.824251 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): -11.36500 43.25800 ymin,ymax (A): 10.88000 54.99200 zmin,zma (A): 36.86500 93.58801 x,y,z range (A): 54.62300 44.11200 56.72300 scale (grids/A): 2.824251 object centre (A): 15.94650 32.93600 65.22650 number of atom coordinates read : 2972 total number of charged atoms : 2825 net assigned charge : -1.999992 assigned positive charge : 445.0956 centred at (gu) : 85.96719 88.09545 95.43390 assigned negative charge : -447.0964 centred at (gu) : 85.85094 87.69853 95.07168 start vw surface at 0.1600000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 198164 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23321 grid for indexing accessible points = 1.400000 m= 102803 mr = 150512 m= 36255 mr = 86071 m= 7863 mr = 29529 m= 962 mr = 5817 m= 24 mr = 616 m= 0 mr = 2 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 1662 time to turn everything in is 1.910000 number of dielectric boundary points 73524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 22599 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) : 1.882834 object centre at (A) : 15.94650 32.93600 65.22650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7739964E-02 0.2099793 midg,1,midg; midg,igrid,midg -5.8092952E-02 0.1164602 1,midg,midg; igrid,midg,midg -0.7035280 0.1861627 gauss-seidel spectral radius is 0.9992598 estimated iterations to convergence 290 setup time was (sec) 2.220000 now iterating at: 13:47:30 rms-change max change #iterations 10.55297 348.8172 at 10iterations 6.196522 142.6246 at 20iterations 3.606454 90.27870 at 30iterations 2.096402 56.20496 at 40iterations 1.214980 23.69262 at 50iterations 0.7026486 13.17047 at 60iterations 0.4061926 6.689235 at 70iterations 0.2339851 3.971468 at 80iterations 0.1350598 2.316299 at 90iterations 7.7869840E-02 1.375715 at 100iterations 4.4811960E-02 0.7319026 at 110iterations 2.5804142E-02 0.4088907 at 120iterations 1.4847592E-02 0.2595768 at 130iterations 8.5861608E-03 0.1472626 at 140iterations 4.9466174E-03 9.0064526E-02 at 150iterations 2.8652509E-03 5.1255226E-02 at 160iterations 1.6645669E-03 2.9977798E-02 at 170iterations 9.7056944E-04 1.6538620E-02 at 180iterations finished qdiffx linear iterations at : 13:47:44 total time elapsed so far: 15.90000 # loops : 180 mean,max change (kT/e) : 9.7056944E-04 1.6538620E-02 energy calculations done at 15.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.08000 DelPhi exited at 13:47:45 16.077u 0.322s 0:16.69 98.2% 0+0k 0+0io 0pf+0w