Mon Oct 10 19:36:27 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 Mon Oct 10 2011 at 19:36:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 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: 0.6767288 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): -17.15800 35.44800 ymin,ymax (A): -7.267000 37.63100 zmin,zma (A): -2.192000 48.91600 x,y,z range (A): 52.60600 44.89800 51.10800 scale (grids/A): 0.6767288 object centre (A): 9.145000 15.18200 23.36200 number of atom coordinates read : 2400 total number of charged atoms : 2264 net assigned charge : 0.5000051 assigned positive charge : 357.9549 centred at (gu) : 92.40385 90.57772 91.03634 assigned negative charge : -357.4555 centred at (gu) : 92.30186 90.76806 91.09943 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7635 nv = 96 ne = 84 npr = 48043 no. pairs analyzed = 48043 no. exposed pairs = 3245 no. arc points = 22120 no. surface atoms = 1086 nbur = 1314 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 571 mr = 4189 m= 5 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3100000 number of dielectric boundary points 3919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2002 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8603 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5396585E-08 -1.9436518E-08 midg,1,midg; midg,igrid,midg 4.7127070E-08 -5.8130297E-08 1,midg,midg; igrid,midg,midg -1.6161318E-08 4.8943853E-08 gauss-seidel spectral radius is 0.9886683 estimated iterations to convergence 77 setup time was (sec) 0.5400000 now iterating at: 19:36:28 rms-change max change #iterations 0.1751358 28.56644 at 10iterations 1.9654252E-02 2.734476 at 20iterations 2.3375496E-03 0.3375587 at 30iterations 3.7586084E-04 5.5473685E-02 at 40iterations 1.0383353E-04 1.5625954E-02 at 50iterations finished qdiffx linear iterations at : 19:36:30 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.0383353E-04 1.5625954E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 19:36:31 3.327u 0.154s 0:03.90 88.9% 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 19:36:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 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: 2.030187 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): -17.15800 35.44800 ymin,ymax (A): -7.267000 37.63100 zmin,zma (A): -2.192000 48.91600 x,y,z range (A): 52.60600 44.89800 51.10800 scale (grids/A): 2.030187 object centre (A): 9.145000 15.18200 23.36200 number of atom coordinates read : 2400 total number of charged atoms : 2264 net assigned charge : 0.5000051 assigned positive charge : 357.9549 centred at (gu) : 97.21101 91.73265 93.10828 assigned negative charge : -357.4555 centred at (gu) : 96.90532 92.30421 93.29810 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22120 grid for indexing accessible points = 1.400000 m= 32865 mr = 56083 m= 6718 mr = 24437 m= 646 mr = 4344 m= 18 mr = 312 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1854 time to turn everything in is 0.6400000 number of dielectric boundary points 36226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 104 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 17949 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) : 0.6767288 object centre at (A) : 9.145000 15.18200 23.36200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7266841E-02 3.0931255E-03 midg,1,midg; midg,igrid,midg 2.6602481E-02 -1.3690667E-02 1,midg,midg; igrid,midg,midg -1.3131543E-02 1.7546063E-02 gauss-seidel spectral radius is 0.9987775 estimated iterations to convergence 226 setup time was (sec) 0.9600000 now iterating at: 19:36:32 rms-change max change #iterations 4.583803 204.1396 at 10iterations 2.221280 76.79843 at 20iterations 1.085889 34.20416 at 30iterations 0.5284643 15.68209 at 40iterations 0.2581122 7.567406 at 50iterations 0.1258601 3.945946 at 60iterations 6.1602086E-02 2.061877 at 70iterations 3.0026563E-02 1.025823 at 80iterations 1.4672461E-02 0.4099884 at 90iterations 7.1621775E-03 0.2010965 at 100iterations 3.5218010E-03 0.1027408 at 110iterations 1.7399023E-03 5.4127693E-02 at 120iterations finished qdiffx linear iterations at : 19:36:39 total time elapsed so far: 8.180000 # loops : 120 mean,max change (kT/e) : 1.7399023E-03 5.4127693E-02 energy calculations done at 8.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.360000 DelPhi exited at 19:36:41 8.367u 0.262s 0:09.42 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 Mon Oct 10 2011 at 19:36:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 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: 3.045280 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): -17.15800 35.44800 ymin,ymax (A): -7.267000 37.63100 zmin,zma (A): -2.192000 48.91600 x,y,z range (A): 52.60600 44.89800 51.10800 scale (grids/A): 3.045280 object centre (A): 9.145000 15.18200 23.36200 number of atom coordinates read : 2400 total number of charged atoms : 2264 net assigned charge : 0.5000051 assigned positive charge : 357.9549 centred at (gu) : 100.8162 92.59880 94.66222 assigned negative charge : -357.4555 centred at (gu) : 100.3579 93.45628 94.94712 start vw surface at 0.1400000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 187140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22120 grid for indexing accessible points = 1.400000 m= 100930 mr = 135826 m= 42650 mr = 82535 m= 12445 mr = 34616 m= 2495 mr = 9261 m= 296 mr = 1786 m= 7 mr = 179 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 5972 time to turn everything in is 1.660000 number of dielectric boundary points 81760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 18112 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) : 2.030187 object centre at (A) : 9.145000 15.18200 23.36200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4490689 0.4467243 midg,1,midg; midg,igrid,midg 0.2028776 4.7441673E-02 1,midg,midg; igrid,midg,midg -5.3843871E-02 6.9522830E-03 gauss-seidel spectral radius is 0.9992956 estimated iterations to convergence 297 setup time was (sec) 2.000000 now iterating at: 19:36:43 rms-change max change #iterations 10.64138 459.8579 at 10iterations 6.323590 142.0495 at 20iterations 3.755628 83.12833 at 30iterations 2.223402 42.99440 at 40iterations 1.310990 26.17368 at 50iterations 0.7717466 15.71228 at 60iterations 0.4527367 9.442116 at 70iterations 0.2660652 5.697797 at 80iterations 0.1553664 2.663294 at 90iterations 9.1161340E-02 1.593985 at 100iterations 5.3156443E-02 0.8984928 at 110iterations 3.1047110E-02 0.5490723 at 120iterations 1.8187027E-02 0.3008595 at 130iterations 1.0603400E-02 0.1962397 at 140iterations 6.2034582E-03 0.1040306 at 150iterations 3.6255335E-03 5.9125900E-02 at 160iterations 2.1264162E-03 3.5778999E-02 at 170iterations 1.2499051E-03 2.3509979E-02 at 180iterations finished qdiffx linear iterations at : 19:36:55 total time elapsed so far: 13.72000 # loops : 180 mean,max change (kT/e) : 1.2499051E-03 2.3509979E-02 energy calculations done at 13.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.91000 DelPhi exited at 19:36:55 13.915u 0.265s 0:14.73 96.1% 0+0k 0+0io 0pf+0w