Mon Oct 10 22:06:19 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 Mon Oct 10 2011 at 22:06:19 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2651 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: 0.5964448 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): 15.88300 75.57000 ymin,ymax (A): -12.36300 43.64000 zmin,zma (A): -7.467000 35.07800 x,y,z range (A): 59.68700 56.00300 42.54500 scale (grids/A): 0.5964448 object centre (A): 45.72650 15.63850 13.80550 number of atom coordinates read : 2651 total number of charged atoms : 2508 net assigned charge : 4.500018 assigned positive charge : 400.5018 centred at (gu) : 89.05299 90.06564 89.79035 assigned negative charge : -396.0024 centred at (gu) : 89.29881 90.20927 89.97410 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6204 nv = 96 ne = 84 npr = 53973 no. pairs analyzed = 53973 no. exposed pairs = 3151 no. arc points = 22003 no. surface atoms = 1074 nbur = 1577 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 291 mr = 3454 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3024 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2180 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 7738 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0115026E-09 -4.3956745E-09 midg,1,midg; midg,igrid,midg 6.2525030E-09 -3.2818914E-09 1,midg,midg; igrid,midg,midg 1.1956927E-08 -5.4411187E-09 gauss-seidel spectral radius is 0.9854545 estimated iterations to convergence 68 setup time was (sec) 0.7200000 now iterating at: 22:06:20 rms-change max change #iterations 0.1088266 17.15211 at 10iterations 1.0333415E-02 1.644604 at 20iterations 1.4409007E-03 0.3179169 at 30iterations 3.6553171E-04 8.9694977E-02 at 40iterations 1.0443348E-04 2.5485992E-02 at 50iterations finished qdiffx linear iterations at : 22:06:24 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 1.0443348E-04 2.5485992E-02 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 22:06:26 4.519u 0.430s 0:06.72 73.5% 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 22:06:26 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2651 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: 1.789334 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): 15.88300 75.57000 ymin,ymax (A): -12.36300 43.64000 zmin,zma (A): -7.467000 35.07800 x,y,z range (A): 59.68700 56.00300 42.54500 scale (grids/A): 1.789334 object centre (A): 45.72650 15.63850 13.80550 number of atom coordinates read : 2651 total number of charged atoms : 2508 net assigned charge : 4.500018 assigned positive charge : 400.5018 centred at (gu) : 87.15839 90.19637 89.37055 assigned negative charge : -396.0024 centred at (gu) : 87.89613 90.62763 89.92194 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 68466 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22003 grid for indexing accessible points = 1.400000 m= 23009 mr = 48247 m= 2926 mr = 16730 m= 93 mr = 1663 m= 0 mr = 13 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1387 time to turn everything in is 0.6700000 number of dielectric boundary points 27841 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 19557 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) : 0.5964448 object centre at (A) : 45.72650 15.63850 13.80550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5103757E-02 1.3113329E-03 midg,1,midg; midg,igrid,midg 2.8600568E-02 -1.7318003E-03 1,midg,midg; igrid,midg,midg -4.4925781E-03 -4.9648520E-02 gauss-seidel spectral radius is 0.9984594 estimated iterations to convergence 202 setup time was (sec) 0.9900000 now iterating at: 22:06:28 rms-change max change #iterations 3.804963 149.8370 at 10iterations 1.693634 59.75489 at 20iterations 0.7561824 26.59059 at 30iterations 0.3383906 11.54887 at 40iterations 0.1514975 5.887093 at 50iterations 6.8170346E-02 2.182022 at 60iterations 3.0553995E-02 1.028112 at 70iterations 1.3758399E-02 0.4687653 at 80iterations 6.2922970E-03 0.2569923 at 90iterations 2.9303408E-03 0.1118469 at 100iterations 1.4263801E-03 5.6068420E-02 at 110iterations 7.2041794E-04 3.2279968E-02 at 120iterations finished qdiffx linear iterations at : 22:06:37 total time elapsed so far: 10.12000 # loops : 120 mean,max change (kT/e) : 7.2041794E-04 3.2279968E-02 energy calculations done at 10.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.35000 DelPhi exited at 22:06:37 10.353u 0.456s 0:11.36 95.0% 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 22:06:37 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2651 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: 2.684002 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): 15.88300 75.57000 ymin,ymax (A): -12.36300 43.64000 zmin,zma (A): -7.467000 35.07800 x,y,z range (A): 59.68700 56.00300 42.54500 scale (grids/A): 2.684002 object centre (A): 45.72650 15.63850 13.80550 number of atom coordinates read : 2651 total number of charged atoms : 2508 net assigned charge : 4.500018 assigned positive charge : 400.5018 centred at (gu) : 85.73737 90.29453 89.05563 assigned negative charge : -396.0024 centred at (gu) : 86.84416 90.94141 89.88287 start vw surface at 0.1600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 159218 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22003 grid for indexing accessible points = 1.400000 m= 77553 mr = 117296 m= 24639 mr = 63389 m= 4863 mr = 19466 m= 435 mr = 3385 m= 5 mr = 260 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 4740 time to turn everything in is 1.750000 number of dielectric boundary points 62917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 20055 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) : 1.789334 object centre at (A) : 45.72650 15.63850 13.80550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2920946 3.8834963E-02 midg,1,midg; midg,igrid,midg 0.3082730 -0.1178803 1,midg,midg; igrid,midg,midg -0.1135941 -0.6728550 gauss-seidel spectral radius is 0.9992087 estimated iterations to convergence 281 setup time was (sec) 2.090000 now iterating at: 22:06:40 rms-change max change #iterations 9.148331 355.3005 at 10iterations 5.214296 115.3458 at 20iterations 2.952163 57.62332 at 30iterations 1.668356 32.82859 at 40iterations 0.9434872 18.88851 at 50iterations 0.5323060 11.57593 at 60iterations 0.3001318 6.255424 at 70iterations 0.1695120 3.240227 at 80iterations 9.5654659E-02 1.910614 at 90iterations 5.3974129E-02 1.021988 at 100iterations 3.0427895E-02 0.6244507 at 110iterations 1.7192049E-02 0.3618469 at 120iterations 9.7857639E-03 0.2092667 at 130iterations 5.6077912E-03 0.1213455 at 140iterations 3.2509228E-03 7.2681427E-02 at 150iterations 1.9343944E-03 4.5902252E-02 at 160iterations 1.1899121E-03 2.8198242E-02 at 170iterations 7.6334545E-04 2.2846222E-02 at 180iterations finished qdiffx linear iterations at : 22:06:55 total time elapsed so far: 16.71000 # loops : 180 mean,max change (kT/e) : 7.6334545E-04 2.2846222E-02 energy calculations done at 16.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.94000 DelPhi exited at 22:06:55 16.947u 0.458s 0:17.78 97.8% 0+0k 0+0io 0pf+0w