Sun Oct 9 19:38:51 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 Sun Oct 9 2011 at 19:38:51 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5896676 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): -11.03300 49.34000 ymin,ymax (A): -12.14500 40.42900 zmin,zma (A): 19.41900 75.80400 x,y,z range (A): 60.37300 52.57400 56.38500 scale (grids/A): 0.5896676 object centre (A): 19.15350 14.14200 47.61150 number of atom coordinates read : 3122 total number of charged atoms : 2975 net assigned charge : 3.121028 assigned positive charge : 484.8942 centred at (gu) : 90.99809 89.52654 87.62407 assigned negative charge : -481.7742 centred at (gu) : 90.89743 89.67252 87.56924 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7293 nv = 96 ne = 84 npr = 60243 no. pairs analyzed = 60243 no. exposed pairs = 4241 no. arc points = 29881 no. surface atoms = 1417 nbur = 1705 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 362 mr = 3626 m= 4 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2926 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5567874E-09 1.5734171E-09 midg,1,midg; midg,igrid,midg 6.2423045E-09 -3.4714884E-09 1,midg,midg; igrid,midg,midg -1.8690034E-09 5.2532143E-09 gauss-seidel spectral radius is 0.9851721 estimated iterations to convergence 67 setup time was (sec) 0.5900000 now iterating at: 19:38:52 rms-change max change #iterations 0.1079104 16.55365 at 10iterations 8.7642260E-03 1.297787 at 20iterations 7.3112873E-04 0.1138220 at 30iterations 9.5262381E-05 1.5319824E-02 at 40iterations 4.0262199E-05 5.6986809E-03 at 50iterations finished qdiffx linear iterations at : 19:38:54 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 4.0262199E-05 5.6986809E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 19:38:55 3.387u 0.147s 0:03.82 92.1% 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 Sun Oct 9 2011 at 19:38:55 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.769003 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): -11.03300 49.34000 ymin,ymax (A): -12.14500 40.42900 zmin,zma (A): 19.41900 75.80400 x,y,z range (A): 60.37300 52.57400 56.38500 scale (grids/A): 1.769003 object centre (A): 19.15350 14.14200 47.61150 number of atom coordinates read : 3122 total number of charged atoms : 2975 net assigned charge : 3.121028 assigned positive charge : 484.8942 centred at (gu) : 92.99372 88.57906 82.87132 assigned negative charge : -481.7742 centred at (gu) : 92.69202 89.01730 82.70726 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 79161 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29881 grid for indexing accessible points = 1.400000 m= 27216 mr = 52522 m= 3885 mr = 18665 m= 167 mr = 1962 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 37239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 205 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 23124 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) : 0.5896676 object centre at (A) : 19.15350 14.14200 47.61150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7843107E-03 6.6308975E-03 midg,1,midg; midg,igrid,midg 2.4746794E-02 -1.4872396E-02 1,midg,midg; igrid,midg,midg -5.3068898E-03 2.0941103E-02 gauss-seidel spectral radius is 0.9984842 estimated iterations to convergence 204 setup time was (sec) 0.8900000 now iterating at: 19:38:56 rms-change max change #iterations 4.195426 208.8606 at 10iterations 1.897245 74.02518 at 20iterations 0.8501762 32.30801 at 30iterations 0.3838786 13.53247 at 40iterations 0.1736932 6.276525 at 50iterations 7.8375794E-02 2.890884 at 60iterations 3.5270717E-02 1.100700 at 70iterations 1.5894452E-02 0.4893818 at 80iterations 7.1932301E-03 0.2483349 at 90iterations 3.2520213E-03 0.1127110 at 100iterations 1.4812828E-03 5.0242424E-02 at 110iterations 6.8432553E-04 2.2216797E-02 at 120iterations finished qdiffx linear iterations at : 19:39:02 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 6.8432553E-04 2.2216797E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 19:39:03 7.511u 0.171s 0:07.98 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 Sun Oct 9 2011 at 19:39:03 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.653504 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): -11.03300 49.34000 ymin,ymax (A): -12.14500 40.42900 zmin,zma (A): 19.41900 75.80400 x,y,z range (A): 60.37300 52.57400 56.38500 scale (grids/A): 2.653504 object centre (A): 19.15350 14.14200 47.61150 number of atom coordinates read : 3122 total number of charged atoms : 2975 net assigned charge : 3.121028 assigned positive charge : 484.8942 centred at (gu) : 94.49029 87.86834 79.30688 assigned negative charge : -481.7742 centred at (gu) : 94.03790 88.52589 79.06084 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 183021 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29881 grid for indexing accessible points = 1.400000 m= 89196 mr = 128398 m= 30480 mr = 69869 m= 6421 mr = 22889 m= 727 mr = 4281 m= 23 mr = 386 m= 0 mr = 2 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.470000 number of dielectric boundary points 84043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 23795 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) : 1.769003 object centre at (A) : 19.15350 14.14200 47.61150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2050609 7.8634977E-02 midg,1,midg; midg,igrid,midg 0.3127060 -0.2749509 1,midg,midg; igrid,midg,midg 0.1853752 0.2661879 gauss-seidel spectral radius is 0.9992399 estimated iterations to convergence 286 setup time was (sec) 1.770000 now iterating at: 19:39:05 rms-change max change #iterations 10.51890 339.7417 at 10iterations 6.224628 197.2653 at 20iterations 3.653413 84.79535 at 30iterations 2.127912 51.49504 at 40iterations 1.234286 31.68628 at 50iterations 0.7123111 16.03863 at 60iterations 0.4108819 8.685453 at 70iterations 0.2360993 4.747009 at 80iterations 0.1356550 2.537489 at 90iterations 7.7923357E-02 1.547913 at 100iterations 4.4742815E-02 0.9411831 at 110iterations 2.5711315E-02 0.5004339 at 120iterations 1.4727823E-02 0.2761879 at 130iterations 8.4537603E-03 0.1710162 at 140iterations 4.8996429E-03 9.3717575E-02 at 150iterations 2.8839139E-03 5.7511330E-02 at 160iterations 1.7572978E-03 3.5021782E-02 at 170iterations 1.1359982E-03 2.1625757E-02 at 180iterations finished qdiffx linear iterations at : 19:39:15 total time elapsed so far: 12.06000 # loops : 180 mean,max change (kT/e) : 1.1359982E-03 2.1625757E-02 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 19:39:16 12.250u 0.195s 0:12.82 97.0% 0+0k 0+0io 0pf+0w