Sun Oct 9 07:49:16 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 07:49:16 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2206 !!! WARNING: NDP 391 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7002360 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): -7.826000 37.57700 ymin,ymax (A): -20.43400 30.40600 zmin,zma (A): -21.38400 23.67700 x,y,z range (A): 45.40300 50.84000 45.06100 scale (grids/A): 0.7002360 object centre (A): 14.87550 4.986000 1.146501 number of atom coordinates read : 2206 total number of charged atoms : 2069 net assigned charge : 5.000016 assigned positive charge : 331.2346 centred at (gu) : 92.13740 90.82419 90.20034 assigned negative charge : -326.2348 centred at (gu) : 92.19046 90.92007 90.34093 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7538 nv = 96 ne = 84 npr = 44821 no. pairs analyzed = 44821 no. exposed pairs = 2713 no. arc points = 19373 no. surface atoms = 925 nbur = 1281 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 517 mr = 4276 m= 3 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 136 time to turn everything in is 0.2700000 number of dielectric boundary points 3689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1818 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8250 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3311670E-08 -2.6975215E-08 midg,1,midg; midg,igrid,midg 6.6403246E-08 -7.2805824E-09 1,midg,midg; igrid,midg,midg 3.9513242E-08 1.8988779E-08 gauss-seidel spectral radius is 0.9893905 estimated iterations to convergence 79 setup time was (sec) 0.5700000 now iterating at: 07:49:16 rms-change max change #iterations 0.2006985 29.92582 at 10iterations 2.3232795E-02 2.954800 at 20iterations 2.9090145E-03 0.4277060 at 30iterations 3.4683460E-04 5.1485062E-02 at 40iterations 4.1539064E-05 7.0773363E-03 at 50iterations finished qdiffx linear iterations at : 07:49:20 total time elapsed so far: 4.120000 # loops : 50 mean,max change (kT/e) : 4.1539064E-05 7.0773363E-03 energy calculations done at 4.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 07:49:20 4.318u 0.276s 0:04.86 94.2% 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 07:49:20 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2206 !!! WARNING: NDP 391 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.100708 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): -7.826000 37.57700 ymin,ymax (A): -20.43400 30.40600 zmin,zma (A): -21.38400 23.67700 x,y,z range (A): 45.40300 50.84000 45.06100 scale (grids/A): 2.100708 object centre (A): 14.87550 4.986000 1.146501 number of atom coordinates read : 2206 total number of charged atoms : 2069 net assigned charge : 5.000016 assigned positive charge : 331.2346 centred at (gu) : 96.41212 92.47234 90.60082 assigned negative charge : -326.2348 centred at (gu) : 96.57122 92.76017 91.02278 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 78802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19373 grid for indexing accessible points = 1.400000 m= 32364 mr = 54959 m= 6569 mr = 24755 m= 682 mr = 4460 m= 30 mr = 350 m= 0 mr = 3 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 3272 time to turn everything in is 0.7200000 number of dielectric boundary points 33920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 16433 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) : 0.7002360 object centre at (A) : 14.87550 4.986000 1.146501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8621206E-02 -2.8250411E-02 midg,1,midg; midg,igrid,midg 3.2654472E-02 5.2061831E-03 1,midg,midg; igrid,midg,midg 2.8783046E-02 2.6718538E-02 gauss-seidel spectral radius is 0.9988279 estimated iterations to convergence 231 setup time was (sec) 1.080000 now iterating at: 07:49:22 rms-change max change #iterations 4.738418 234.7795 at 10iterations 2.334920 84.23180 at 20iterations 1.152757 35.72026 at 30iterations 0.5713510 17.24030 at 40iterations 0.2833319 9.564690 at 50iterations 0.1404930 4.121093 at 60iterations 6.9535300E-02 1.984523 at 70iterations 3.4424890E-02 1.026695 at 80iterations 1.7042346E-02 0.5878220 at 90iterations 8.4368028E-03 0.2522678 at 100iterations 4.1774884E-03 0.1244459 at 110iterations 2.0658693E-03 6.0525894E-02 at 120iterations finished qdiffx linear iterations at : 07:49:31 total time elapsed so far: 9.960000 # loops : 120 mean,max change (kT/e) : 2.0658693E-03 6.0525894E-02 energy calculations done at 9.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.15000 DelPhi exited at 07:49:31 10.150u 0.317s 0:10.84 96.4% 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 07:49:31 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2206 !!! WARNING: NDP 391 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.151062 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): -7.826000 37.57700 ymin,ymax (A): -20.43400 30.40600 zmin,zma (A): -21.38400 23.67700 x,y,z range (A): 45.40300 50.84000 45.06100 scale (grids/A): 3.151062 object centre (A): 14.87550 4.986000 1.146501 number of atom coordinates read : 2206 total number of charged atoms : 2069 net assigned charge : 5.000016 assigned positive charge : 331.2346 centred at (gu) : 99.61806 93.70847 90.90109 assigned negative charge : -326.2348 centred at (gu) : 99.85675 94.14022 91.53419 start vw surface at 0.1700000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 181669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19373 grid for indexing accessible points = 1.400000 m= 99054 mr = 132305 m= 42139 mr = 82801 m= 12493 mr = 34906 m= 2552 mr = 9747 m= 373 mr = 1816 m= 17 mr = 244 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 10622 time to turn everything in is 2.060000 number of dielectric boundary points 76475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 16552 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) : 2.100708 object centre at (A) : 14.87550 4.986000 1.146501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3193901 -0.2877842 midg,1,midg; midg,igrid,midg 0.3224645 0.1981163 1,midg,midg; igrid,midg,midg 0.2592025 0.2691743 gauss-seidel spectral radius is 0.9992960 estimated iterations to convergence 297 setup time was (sec) 2.440000 now iterating at: 07:49:34 rms-change max change #iterations 10.44567 471.2649 at 10iterations 6.104586 120.2729 at 20iterations 3.565242 73.75645 at 30iterations 2.081669 37.73067 at 40iterations 1.215373 22.21475 at 50iterations 0.7062494 12.80318 at 60iterations 0.4121434 8.065842 at 70iterations 0.2402521 4.037180 at 80iterations 0.1397635 2.656385 at 90iterations 8.1300177E-02 1.271717 at 100iterations 4.7282659E-02 0.8109856 at 110iterations 2.7594164E-02 0.4539566 at 120iterations 1.6034665E-02 0.2615373 at 130iterations 9.3307104E-03 0.1744595 at 140iterations 5.4389155E-03 9.4362259E-02 at 150iterations 3.1619337E-03 5.6148529E-02 at 160iterations 1.8414019E-03 3.2604218E-02 at 170iterations 1.0690842E-03 1.7686844E-02 at 180iterations finished qdiffx linear iterations at : 07:49:48 total time elapsed so far: 16.67000 # loops : 180 mean,max change (kT/e) : 1.0690842E-03 1.7686844E-02 energy calculations done at 16.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.85000 DelPhi exited at 07:49:49 16.849u 0.349s 0:17.48 98.2% 0+0k 0+0io 0pf+0w