Tue Oct 11 03:41:03 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 Tue Oct 11 2011 at 03:41:03 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2649 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: 0.6635478 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): -14.85600 33.84000 ymin,ymax (A): 7.072999 55.57000 zmin,zma (A): 25.94700 79.59800 x,y,z range (A): 48.69600 48.49700 53.65100 scale (grids/A): 0.6635478 object centre (A): 9.492001 31.32150 52.77250 number of atom coordinates read : 2649 total number of charged atoms : 2501 net assigned charge : 2.500012 assigned positive charge : 402.1259 centred at (gu) : 89.95401 90.17662 88.51975 assigned negative charge : -399.6264 centred at (gu) : 90.18389 89.98616 88.57598 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7893 nv = 96 ne = 84 npr = 53837 no. pairs analyzed = 53837 no. exposed pairs = 3181 no. arc points = 22341 no. surface atoms = 1073 nbur = 1576 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 4562 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.3500000 number of dielectric boundary points 3736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2151 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9230 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6183809E-08 -4.1773780E-09 midg,1,midg; midg,igrid,midg -3.5141476E-08 5.0156231E-08 1,midg,midg; igrid,midg,midg 5.7277305E-08 -4.5222297E-08 gauss-seidel spectral radius is 0.9882302 estimated iterations to convergence 75 setup time was (sec) 0.6300000 now iterating at: 03:41:04 rms-change max change #iterations 0.1728457 21.34327 at 10iterations 1.9104945E-02 2.582771 at 20iterations 2.1526916E-03 0.2679596 at 30iterations 2.7075681E-04 3.9310455E-02 at 40iterations 5.1425810E-05 6.9198608E-03 at 50iterations finished qdiffx linear iterations at : 03:41:07 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 5.1425810E-05 6.9198608E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 03:41:08 4.076u 0.259s 0:04.75 90.9% 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 Tue Oct 11 2011 at 03:41:08 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2649 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: 1.990643 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): -14.85600 33.84000 ymin,ymax (A): 7.072999 55.57000 zmin,zma (A): 25.94700 79.59800 x,y,z range (A): 48.69600 48.49700 53.65100 scale (grids/A): 1.990643 object centre (A): 9.492001 31.32150 52.77250 number of atom coordinates read : 2649 total number of charged atoms : 2501 net assigned charge : 2.500012 assigned positive charge : 402.1259 centred at (gu) : 89.86134 90.52930 85.55862 assigned negative charge : -399.6264 centred at (gu) : 90.55152 89.95812 85.72746 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 85013 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22341 grid for indexing accessible points = 1.400000 m= 32464 mr = 60585 m= 5586 mr = 24568 m= 428 mr = 3761 m= 12 mr = 191 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1375 time to turn everything in is 0.7400000 number of dielectric boundary points 34398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 19731 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) : 0.6635478 object centre at (A) : 9.492001 31.32150 52.77250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3489696E-03 -3.0089736E-02 midg,1,midg; midg,igrid,midg -1.7048053E-02 4.8829153E-02 1,midg,midg; igrid,midg,midg 6.5055512E-02 -1.5136083E-02 gauss-seidel spectral radius is 0.9987512 estimated iterations to convergence 224 setup time was (sec) 1.030000 now iterating at: 03:41:09 rms-change max change #iterations 4.735891 217.3678 at 10iterations 2.302813 69.13223 at 20iterations 1.113100 35.39109 at 30iterations 0.5428315 18.94881 at 40iterations 0.2622960 7.480963 at 50iterations 0.1276390 3.897900 at 60iterations 6.1738633E-02 1.931977 at 70iterations 2.9963072E-02 0.8233778 at 80iterations 1.4595108E-02 0.4371700 at 90iterations 7.0800157E-03 0.2222519 at 100iterations 3.4574261E-03 0.1058459 at 110iterations 1.6990784E-03 4.5841217E-02 at 120iterations finished qdiffx linear iterations at : 03:41:18 total time elapsed so far: 9.330000 # loops : 120 mean,max change (kT/e) : 1.6990784E-03 4.5841217E-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 03:41:19 9.515u 0.306s 0:10.68 91.8% 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 Tue Oct 11 2011 at 03:41:19 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2649 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: 2.985965 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): -14.85600 33.84000 ymin,ymax (A): 7.072999 55.57000 zmin,zma (A): 25.94700 79.59800 x,y,z range (A): 48.69600 48.49700 53.65100 scale (grids/A): 2.985965 object centre (A): 9.492001 31.32150 52.77250 number of atom coordinates read : 2649 total number of charged atoms : 2501 net assigned charge : 2.500012 assigned positive charge : 402.1259 centred at (gu) : 89.79200 90.79388 83.33801 assigned negative charge : -399.6264 centred at (gu) : 90.82724 89.93723 83.59107 start vw surface at 0.1600000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 196213 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22341 grid for indexing accessible points = 1.400000 m= 103725 mr = 145766 m= 39547 mr = 86600 m= 10442 mr = 32555 m= 1870 mr = 8048 m= 132 mr = 1362 m= 1 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 4609 time to turn everything in is 1.980000 number of dielectric boundary points 77533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 20004 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) : 1.990643 object centre at (A) : 9.492001 31.32150 52.77250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1952270 -0.3619927 midg,1,midg; midg,igrid,midg -0.1793451 0.5372118 1,midg,midg; igrid,midg,midg 0.5580357 -0.1223987 gauss-seidel spectral radius is 0.9992838 estimated iterations to convergence 295 setup time was (sec) 2.310000 now iterating at: 03:41:21 rms-change max change #iterations 10.81942 549.7002 at 10iterations 6.359228 136.0984 at 20iterations 3.732366 67.75459 at 30iterations 2.182522 43.49266 at 40iterations 1.278013 24.23748 at 50iterations 0.7456347 14.28827 at 60iterations 0.4354974 7.656433 at 70iterations 0.2538690 5.082638 at 80iterations 0.1481302 2.638053 at 90iterations 8.6204588E-02 1.437574 at 100iterations 5.0228816E-02 0.8577805 at 110iterations 2.9263763E-02 0.4800472 at 120iterations 1.7059110E-02 0.2853279 at 130iterations 9.9910758E-03 0.1706324 at 140iterations 5.8712545E-03 0.1033325 at 150iterations 3.4812326E-03 6.3756943E-02 at 160iterations 2.1015054E-03 3.6994934E-02 at 170iterations 1.2944444E-03 2.5299072E-02 at 180iterations finished qdiffx linear iterations at : 03:41:35 total time elapsed so far: 16.05000 # loops : 180 mean,max change (kT/e) : 1.2944444E-03 2.5299072E-02 energy calculations done at 16.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.23000 DelPhi exited at 03:41:36 16.230u 0.296s 0:17.02 97.0% 0+0k 0+0io 0pf+0w