Sun Oct 9 12:29:50 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 12:29:51 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2394 !!! WARNING: GLM 235 has a net charge of -0.0940 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: 0.6761761 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): -5.530000 44.48800 ymin,ymax (A): -13.98100 38.66800 zmin,zma (A): 2.472000 45.41100 x,y,z range (A): 50.01800 52.64900 42.93900 scale (grids/A): 0.6761761 object centre (A): 19.47900 12.34350 23.94150 number of atom coordinates read : 2394 total number of charged atoms : 2247 net assigned charge : 1.406025 assigned positive charge : 365.9540 centred at (gu) : 89.28767 90.59853 90.50001 assigned negative charge : -364.5485 centred at (gu) : 89.29509 90.83805 90.54716 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7328 nv = 96 ne = 84 npr = 47940 no. pairs analyzed = 47940 no. exposed pairs = 3011 no. arc points = 20891 no. surface atoms = 1012 nbur = 1382 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 4080 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.2700000 number of dielectric boundary points 3604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1932 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8516 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7273509E-08 -7.9277553E-09 midg,1,midg; midg,igrid,midg 6.2840051E-08 -7.0600080E-08 1,midg,midg; igrid,midg,midg 9.3856958E-09 3.4984931E-09 gauss-seidel spectral radius is 0.9886402 estimated iterations to convergence 77 setup time was (sec) 0.5100000 now iterating at: 12:29:51 rms-change max change #iterations 0.1780670 25.62416 at 10iterations 2.0420427E-02 2.590162 at 20iterations 2.7540515E-03 0.3725319 at 30iterations 5.5585016E-04 8.9401245E-02 at 40iterations 1.6147672E-04 2.2792816E-02 at 50iterations finished qdiffx linear iterations at : 12:29:54 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.6147672E-04 2.2792816E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 12:29:54 3.335u 0.198s 0:03.80 92.6% 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 12:29:54 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 = 2394 !!! WARNING: GLM 235 has a net charge of -0.0940 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: 2.028528 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): -5.530000 44.48800 ymin,ymax (A): -13.98100 38.66800 zmin,zma (A): 2.472000 45.41100 x,y,z range (A): 50.01800 52.64900 42.93900 scale (grids/A): 2.028528 object centre (A): 19.47900 12.34350 23.94150 number of atom coordinates read : 2394 total number of charged atoms : 2247 net assigned charge : 1.406025 assigned positive charge : 365.9540 centred at (gu) : 87.86268 91.79487 91.49957 assigned negative charge : -364.5485 centred at (gu) : 87.88514 92.51379 91.64132 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20891 grid for indexing accessible points = 1.400000 m= 29652 mr = 54807 m= 5061 mr = 22085 m= 357 mr = 3282 m= 5 mr = 152 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 3348 time to turn everything in is 0.5500000 number of dielectric boundary points 33366 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17780 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) : 0.6761761 object centre at (A) : 19.47900 12.34350 23.94150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6028448E-02 5.5122399E-03 midg,1,midg; midg,igrid,midg 1.8256707E-02 -9.2259303E-02 1,midg,midg; igrid,midg,midg 4.5047294E-02 -6.9710063E-03 gauss-seidel spectral radius is 0.9987707 estimated iterations to convergence 226 setup time was (sec) 0.8600000 now iterating at: 12:29:55 rms-change max change #iterations 4.661788 194.2731 at 10iterations 2.257180 76.17000 at 20iterations 1.094640 34.88563 at 30iterations 0.5332106 18.53176 at 40iterations 0.2594175 7.720295 at 50iterations 0.1264803 4.045073 at 60iterations 6.1709393E-02 1.792105 at 70iterations 3.0157553E-02 0.9221840 at 80iterations 1.4883111E-02 0.4745827 at 90iterations 7.4003795E-03 0.2469635 at 100iterations 3.7408741E-03 0.1371584 at 110iterations 1.9548296E-03 6.0829163E-02 at 120iterations finished qdiffx linear iterations at : 12:30:02 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 1.9548296E-03 6.0829163E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 12:30:03 7.663u 0.210s 0:08.18 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 12:30:03 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2394 !!! WARNING: GLM 235 has a net charge of -0.0940 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: 3.042793 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): -5.530000 44.48800 ymin,ymax (A): -13.98100 38.66800 zmin,zma (A): 2.472000 45.41100 x,y,z range (A): 50.01800 52.64900 42.93900 scale (grids/A): 3.042793 object centre (A): 19.47900 12.34350 23.94150 number of atom coordinates read : 2394 total number of charged atoms : 2247 net assigned charge : 1.406025 assigned positive charge : 365.9540 centred at (gu) : 86.79389 92.69225 92.24936 assigned negative charge : -364.5485 centred at (gu) : 86.82773 93.77062 92.46186 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 181484 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20891 grid for indexing accessible points = 1.400000 m= 94554 mr = 132603 m= 35756 mr = 77685 m= 9261 mr = 29089 m= 1626 mr = 7060 m= 149 mr = 1141 m= 1 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 10865 time to turn everything in is 1.430000 number of dielectric boundary points 75167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 17976 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) : 2.028528 object centre at (A) : 19.47900 12.34350 23.94150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3792793 -1.5008725E-02 midg,1,midg; midg,igrid,midg 0.4483089 -1.022724 1,midg,midg; igrid,midg,midg 0.4743921 -0.2482240 gauss-seidel spectral radius is 0.9992841 estimated iterations to convergence 295 setup time was (sec) 1.750000 now iterating at: 12:30:05 rms-change max change #iterations 10.63188 494.9053 at 10iterations 6.259762 132.4944 at 20iterations 3.694919 84.32961 at 30iterations 2.165263 41.19548 at 40iterations 1.267637 24.30425 at 50iterations 0.7409099 13.67093 at 60iterations 0.4340101 8.138161 at 70iterations 0.2529444 4.779124 at 80iterations 0.1472692 2.708174 at 90iterations 8.6027585E-02 1.552538 at 100iterations 5.0316874E-02 0.8864441 at 110iterations 2.9456735E-02 0.5094357 at 120iterations 1.7351106E-02 0.3273315 at 130iterations 1.0380737E-02 0.1966095 at 140iterations 6.3369954E-03 0.1210709 at 150iterations 4.0152865E-03 8.2000732E-02 at 160iterations 2.6748783E-03 5.7586670E-02 at 170iterations 1.8930362E-03 4.0471077E-02 at 180iterations finished qdiffx linear iterations at : 12:30:15 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 1.8930362E-03 4.0471077E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 12:30:16 12.589u 0.255s 0:13.13 97.7% 0+0k 0+0io 0pf+0w