Mon Oct 10 23:52:09 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 23:52:09 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 = 2712 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: 0.5915194 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): 14.82800 75.01200 ymin,ymax (A): -10.88300 43.71200 zmin,zma (A): -7.584000 34.88200 x,y,z range (A): 60.18400 54.59500 42.46600 scale (grids/A): 0.5915194 object centre (A): 44.92000 16.41450 13.64900 number of atom coordinates read : 2712 total number of charged atoms : 2569 net assigned charge : 4.500022 assigned positive charge : 409.8555 centred at (gu) : 89.27485 89.80013 89.93402 assigned negative charge : -405.3563 centred at (gu) : 89.54985 89.93740 90.10312 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6117 nv = 96 ne = 84 npr = 55509 no. pairs analyzed = 55509 no. exposed pairs = 3179 no. arc points = 22247 no. surface atoms = 1077 nbur = 1635 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 268 mr = 3379 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.4300000 number of dielectric boundary points 2986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2203 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 7766 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3382593E-09 -3.5834937E-09 midg,1,midg; midg,igrid,midg 5.5979843E-09 -2.5508624E-09 1,midg,midg; igrid,midg,midg 1.0870470E-08 -5.8136198E-09 gauss-seidel spectral radius is 0.9852160 estimated iterations to convergence 67 setup time was (sec) 0.7100000 now iterating at: 23:52:10 rms-change max change #iterations 0.1062650 16.68199 at 10iterations 9.1525745E-03 1.484957 at 20iterations 1.1559541E-03 0.2465820 at 30iterations 2.6265997E-04 6.5624237E-02 at 40iterations 6.9483976E-05 1.7875671E-02 at 50iterations finished qdiffx linear iterations at : 23:52:13 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 6.9483976E-05 1.7875671E-02 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 23:52:14 4.082u 0.159s 0:04.71 89.8% 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 Mon Oct 10 2011 at 23:52:14 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 = 2712 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: 1.774558 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): 14.82800 75.01200 ymin,ymax (A): -10.88300 43.71200 zmin,zma (A): -7.584000 34.88200 x,y,z range (A): 60.18400 54.59500 42.46600 scale (grids/A): 1.774558 object centre (A): 44.92000 16.41450 13.64900 number of atom coordinates read : 2712 total number of charged atoms : 2569 net assigned charge : 4.500022 assigned positive charge : 409.8555 centred at (gu) : 87.82381 89.39971 89.80164 assigned negative charge : -405.3563 centred at (gu) : 88.64913 89.81181 90.30898 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 67724 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22247 grid for indexing accessible points = 1.400000 m= 22049 mr = 47404 m= 2745 mr = 16091 m= 105 mr = 1608 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 690 time to turn everything in is 0.6500000 number of dielectric boundary points 27502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20026 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) : 0.5915194 object centre at (A) : 44.92000 16.41450 13.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3663528E-02 4.8366031E-03 midg,1,midg; midg,igrid,midg 3.1359255E-02 -1.7843146E-02 1,midg,midg; igrid,midg,midg 6.7254365E-04 -5.7596225E-02 gauss-seidel spectral radius is 0.9984382 estimated iterations to convergence 201 setup time was (sec) 0.9800000 now iterating at: 23:52:15 rms-change max change #iterations 3.792979 176.9447 at 10iterations 1.675870 62.65195 at 20iterations 0.7462542 27.79316 at 30iterations 0.3318433 11.21281 at 40iterations 0.1476653 5.018192 at 50iterations 6.5624312E-02 2.253780 at 60iterations 2.9219659E-02 0.9843655 at 70iterations 1.3115933E-02 0.5021193 at 80iterations 5.9595103E-03 0.2141953 at 90iterations 2.7723301E-03 9.9388123E-02 at 100iterations 1.3315737E-03 5.4428101E-02 at 110iterations 6.7433581E-04 2.9666901E-02 at 120iterations finished qdiffx linear iterations at : 23:52:23 total time elapsed so far: 8.610000 # loops : 120 mean,max change (kT/e) : 6.7433581E-04 2.9666901E-02 energy calculations done at 8.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.860000 DelPhi exited at 23:52:23 8.865u 0.204s 0:09.58 94.5% 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 23:52:24 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 = 2712 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: 2.661837 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): 14.82800 75.01200 ymin,ymax (A): -10.88300 43.71200 zmin,zma (A): -7.584000 34.88200 x,y,z range (A): 60.18400 54.59500 42.46600 scale (grids/A): 2.661837 object centre (A): 44.92000 16.41450 13.64900 number of atom coordinates read : 2712 total number of charged atoms : 2569 net assigned charge : 4.500022 assigned positive charge : 409.8555 centred at (gu) : 86.73564 89.09937 89.70223 assigned negative charge : -405.3563 centred at (gu) : 87.97358 89.71765 90.46351 start vw surface at 0.2200000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 157081 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22247 grid for indexing accessible points = 1.400000 m= 74713 mr = 115215 m= 23261 mr = 60824 m= 4483 mr = 18443 m= 459 mr = 3245 m= 5 mr = 302 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 2266 time to turn everything in is 1.540000 number of dielectric boundary points 61973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 20546 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) : 1.774558 object centre at (A) : 44.92000 16.41450 13.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2641810 7.8040816E-02 midg,1,midg; midg,igrid,midg 0.4688399 -0.3009059 1,midg,midg; igrid,midg,midg -7.1922638E-02 -0.8243372 gauss-seidel spectral radius is 0.9992008 estimated iterations to convergence 279 setup time was (sec) 1.900000 now iterating at: 23:52:26 rms-change max change #iterations 9.137398 256.5465 at 10iterations 5.182662 112.2781 at 20iterations 2.925310 68.56027 at 30iterations 1.654199 34.96637 at 40iterations 0.9331154 18.61619 at 50iterations 0.5247930 11.95113 at 60iterations 0.2956101 6.011345 at 70iterations 0.1657629 3.224487 at 80iterations 9.3713239E-02 1.731892 at 90iterations 5.2650180E-02 0.9889109 at 100iterations 2.9590819E-02 0.6113091 at 110iterations 1.6677300E-02 0.3124390 at 120iterations 9.4603645E-03 0.2107372 at 130iterations 5.3582853E-03 0.1084576 at 140iterations 3.0764856E-03 6.3194275E-02 at 150iterations 1.7911323E-03 4.2613983E-02 at 160iterations 1.0808696E-03 2.6397705E-02 at 170iterations 6.7714672E-04 1.7124176E-02 at 180iterations finished qdiffx linear iterations at : 23:52:37 total time elapsed so far: 13.78000 # loops : 180 mean,max change (kT/e) : 6.7714672E-04 1.7124176E-02 energy calculations done at 13.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.04000 DelPhi exited at 23:52:38 14.040u 0.219s 0:14.59 97.6% 0+0k 0+0io 0pf+0w