Sun Oct 9 17:22:06 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 Sun Oct 9 2011 at 17:22:07 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5220 !!! 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5488660 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): 3.269000 68.13000 ymin,ymax (A): -8.585000 53.49400 zmin,zma (A): -1.236000 62.02600 x,y,z range (A): 64.86101 62.07900 63.26200 scale (grids/A): 0.5488660 object centre (A): 35.69950 22.45450 30.39500 number of atom coordinates read : 5220 total number of charged atoms : 5068 net assigned charge : 0.6210474 assigned positive charge : 801.0493 centred at (gu) : 88.11424 89.06349 89.53357 assigned negative charge : -800.4345 centred at (gu) : 87.95779 89.11210 89.47417 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 10256 nv = 96 ne = 84 npr = 106248 no. pairs analyzed = 106248 no. exposed pairs = 6166 no. arc points = 41837 no. surface atoms = 2107 nbur = 3113 mkacc time = 0.2500000 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 = 1.568000 m= 437 mr = 5848 m= 1 mr = 24 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 0.5300000 number of dielectric boundary points 4822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4257 ## 508 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 13511 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.9423640E-10 7.7154499E-10 midg,1,midg; midg,igrid,midg 9.1816482E-10 -4.4404455E-10 1,midg,midg; igrid,midg,midg -3.2715601E-09 1.3280619E-09 gauss-seidel spectral radius is 0.9830441 estimated iterations to convergence 63 setup time was (sec) 0.7900000 now iterating at: 17:22:07 rms-change max change #iterations 0.1059317 14.89977 at 10iterations 9.9130701E-03 1.287025 at 20iterations 2.9686193E-03 0.3298340 at 30iterations 1.3749857E-03 0.1499681 at 40iterations 6.6514179E-04 7.9440117E-02 at 50iterations finished qdiffx linear iterations at : 17:22:10 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 6.6514179E-04 7.9440117E-02 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 17:22:11 3.713u 0.155s 0:04.14 93.2% 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 17:22:11 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5220 !!! 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.646598 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): 3.269000 68.13000 ymin,ymax (A): -8.585000 53.49400 zmin,zma (A): -1.236000 62.02600 x,y,z range (A): 64.86101 62.07900 63.26200 scale (grids/A): 1.646598 object centre (A): 35.69950 22.45450 30.39500 number of atom coordinates read : 5220 total number of charged atoms : 5068 net assigned charge : 0.6210474 assigned positive charge : 801.0493 centred at (gu) : 84.34110 87.18941 88.59910 assigned negative charge : -800.4345 centred at (gu) : 83.87319 87.33614 88.42267 start vw surface at 0.2200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 114120 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41837 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 39335 mr = 82566 m= 4599 mr = 28312 m= 134 mr = 2457 m= 0 mr = 9 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 44844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 425 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 38911 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) : 0.5488660 object centre at (A) : 35.69950 22.45450 30.39500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4440354E-02 -8.4638642E-03 midg,1,midg; midg,igrid,midg 1.6874840E-02 7.0278132E-03 1,midg,midg; igrid,midg,midg -3.1506728E-02 1.7189570E-02 gauss-seidel spectral radius is 0.9984171 estimated iterations to convergence 199 setup time was (sec) 1.150000 now iterating at: 17:22:12 rms-change max change #iterations 4.775255 167.2195 at 10iterations 2.107301 57.74834 at 20iterations 0.9338028 26.65377 at 30iterations 0.4134138 11.58305 at 40iterations 0.1841342 6.266350 at 50iterations 8.1789225E-02 2.152861 at 60iterations 3.6753491E-02 1.050920 at 70iterations 1.6927393E-02 0.4713135 at 80iterations 8.4003620E-03 0.2496719 at 90iterations 4.6527912E-03 0.1357352 at 100iterations 2.9653695E-03 7.7934265E-02 at 110iterations 2.1135435E-03 5.1019669E-02 at 120iterations finished qdiffx linear iterations at : 17:22:19 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 2.1135435E-03 5.1019669E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.250000 DelPhi exited at 17:22:19 8.250u 0.160s 0:08.73 96.3% 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 17:22:20 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5220 !!! 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.469897 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): 3.269000 68.13000 ymin,ymax (A): -8.585000 53.49400 zmin,zma (A): -1.236000 62.02600 x,y,z range (A): 64.86101 62.07900 63.26200 scale (grids/A): 2.469897 object centre (A): 35.69950 22.45450 30.39500 number of atom coordinates read : 5220 total number of charged atoms : 5068 net assigned charge : 0.6210474 assigned positive charge : 801.0493 centred at (gu) : 81.51147 85.78362 87.89818 assigned negative charge : -800.4345 centred at (gu) : 80.80973 86.00426 87.63400 start vw surface at 0.2200000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 265206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41837 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 132927 mr = 200815 m= 41550 mr = 108336 m= 7469 mr = 32027 m= 608 mr = 5126 m= 16 mr = 279 m= 0 mr = 0 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.120000 number of dielectric boundary points 101193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 2.270000 number of grid points assigned charge 40505 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) : 1.646598 object centre at (A) : 35.69950 22.45450 30.39500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3727090 -0.2562617 midg,1,midg; midg,igrid,midg 8.5276060E-02 -1.9925408E-02 1,midg,midg; igrid,midg,midg -0.5162310 0.2129685 gauss-seidel spectral radius is 0.9992510 estimated iterations to convergence 288 setup time was (sec) 2.460000 now iterating at: 17:22:22 rms-change max change #iterations 12.17842 374.1331 at 10iterations 7.185010 162.9903 at 20iterations 4.198268 87.44532 at 30iterations 2.445026 44.38056 at 40iterations 1.419069 24.97022 at 50iterations 0.8225020 14.55061 at 60iterations 0.4753650 7.731049 at 70iterations 0.2747775 4.281040 at 80iterations 0.1583216 2.410503 at 90iterations 9.1298737E-02 1.557383 at 100iterations 5.2795831E-02 0.8365231 at 110iterations 3.0568177E-02 0.5462818 at 120iterations 1.7933609E-02 0.2897720 at 130iterations 1.0726056E-02 0.1748047 at 140iterations 6.6671274E-03 0.1118984 at 150iterations 4.3865945E-03 7.3879242E-02 at 160iterations 3.1081368E-03 4.9575806E-02 at 170iterations 2.3617437E-03 3.5561562E-02 at 180iterations finished qdiffx linear iterations at : 17:22:33 total time elapsed so far: 13.18000 # loops : 180 mean,max change (kT/e) : 2.3617437E-03 3.5561562E-02 energy calculations done at 13.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.38000 DelPhi exited at 17:22:33 13.385u 0.202s 0:13.92 97.5% 0+0k 0+0io 0pf+0w