Mon Oct 10 16:04:19 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 16:04:19 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4881 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5241461 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): 7.872000 62.48300 ymin,ymax (A): -26.26200 41.65800 zmin,zma (A): -28.85800 33.44400 x,y,z range (A): 54.61100 67.92000 62.30200 scale (grids/A): 0.5241461 object centre (A): 35.17750 7.697998 2.293000 number of atom coordinates read : 4881 total number of charged atoms : 4723 net assigned charge : 2.028033 assigned positive charge : 733.3241 centred at (gu) : 89.61253 89.33960 89.27874 assigned negative charge : -731.3003 centred at (gu) : 89.61237 89.39491 89.28956 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8425 nv = 96 ne = 84 npr = 100450 no. pairs analyzed = 100450 no. exposed pairs = 5990 no. arc points = 39794 no. surface atoms = 2035 nbur = 2846 mkacc time = 0.2800000 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 = 1.624000 m= 315 mr = 4605 m= 0 mr = 3 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3948 ## 505 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 11359 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2023564E-10 -5.1962796E-13 midg,1,midg; midg,igrid,midg 3.6320372E-10 -1.7693380E-10 1,midg,midg; igrid,midg,midg 5.3705981E-11 4.5634174E-11 gauss-seidel spectral radius is 0.9813818 estimated iterations to convergence 60 setup time was (sec) 0.8300000 now iterating at: 16:04:20 rms-change max change #iterations 7.9092123E-02 11.13078 at 10iterations 5.7618343E-03 0.7822647 at 20iterations 1.4951838E-03 0.1980209 at 30iterations 6.6587690E-04 9.2782974E-02 at 40iterations 3.0805185E-04 4.3836594E-02 at 50iterations finished qdiffx linear iterations at : 16:04:23 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 3.0805185E-04 4.3836594E-02 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 16:04:24 4.311u 0.262s 0:04.89 93.4% 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 Mon Oct 10 2011 at 16:04:24 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4881 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.572438 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): 7.872000 62.48300 ymin,ymax (A): -26.26200 41.65800 zmin,zma (A): -28.85800 33.44400 x,y,z range (A): 54.61100 67.92000 62.30200 scale (grids/A): 1.572438 object centre (A): 35.17750 7.697998 2.293000 number of atom coordinates read : 4881 total number of charged atoms : 4723 net assigned charge : 2.028033 assigned positive charge : 733.3241 centred at (gu) : 88.83589 88.01707 87.83447 assigned negative charge : -731.3003 centred at (gu) : 88.83669 88.18404 87.86790 start vw surface at 0.2200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 96354 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39794 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 29487 mr = 68455 m= 2792 mr = 20234 m= 56 mr = 1272 m= 0 mr = 6 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 719 time to turn everything in is 0.8500000 number of dielectric boundary points 38722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 460 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 35758 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) : 0.5241461 object centre at (A) : 35.17750 7.697998 2.293000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7018811E-03 -1.2068251E-02 midg,1,midg; midg,igrid,midg 2.7593801E-02 -1.9040652E-02 1,midg,midg; igrid,midg,midg 2.6686350E-03 2.7574976E-03 gauss-seidel spectral radius is 0.9982237 estimated iterations to convergence 188 setup time was (sec) 1.160000 now iterating at: 16:04:25 rms-change max change #iterations 4.083817 143.2479 at 10iterations 1.716149 54.03400 at 20iterations 0.7233826 22.83276 at 30iterations 0.3054103 9.389763 at 40iterations 0.1287221 3.904106 at 50iterations 5.4574329E-02 1.643791 at 60iterations 2.3328453E-02 0.7105484 at 70iterations 1.0179740E-02 0.3320389 at 80iterations 4.7550108E-03 0.1376343 at 90iterations 2.4980849E-03 7.8044891E-02 at 100iterations 1.5328135E-03 4.6745300E-02 at 110iterations 1.0627646E-03 3.1171799E-02 at 120iterations finished qdiffx linear iterations at : 16:04:34 total time elapsed so far: 9.550000 # loops : 120 mean,max change (kT/e) : 1.0627646E-03 3.1171799E-02 energy calculations done at 9.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.730000 DelPhi exited at 16:04:34 9.735u 0.283s 0:10.30 97.1% 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 16:04:34 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4881 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.358657 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): 7.872000 62.48300 ymin,ymax (A): -26.26200 41.65800 zmin,zma (A): -28.85800 33.44400 x,y,z range (A): 54.61100 67.92000 62.30200 scale (grids/A): 2.358657 object centre (A): 35.17750 7.697998 2.293000 number of atom coordinates read : 4881 total number of charged atoms : 4723 net assigned charge : 2.028033 assigned positive charge : 733.3241 centred at (gu) : 88.25346 87.02528 86.75148 assigned negative charge : -731.3003 centred at (gu) : 88.25495 87.27599 86.80176 start vw surface at 0.2100000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 224281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39794 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 104321 mr = 167557 m= 28250 mr = 82417 m= 4146 mr = 21180 m= 237 mr = 2608 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 2404 time to turn everything in is 2.100000 number of dielectric boundary points 87410 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 37695 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) : 1.572438 object centre at (A) : 35.17750 7.697998 2.293000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4574239E-02 -0.2718117 midg,1,midg; midg,igrid,midg 0.6665701 -0.6832809 1,midg,midg; igrid,midg,midg 7.8640595E-02 8.0099836E-02 gauss-seidel spectral radius is 0.9991955 estimated iterations to convergence 278 setup time was (sec) 2.430000 now iterating at: 16:04:37 rms-change max change #iterations 10.93632 385.8566 at 10iterations 6.336820 159.5203 at 20iterations 3.652790 86.84406 at 30iterations 2.094662 40.45199 at 40iterations 1.197119 22.62608 at 50iterations 0.6807790 12.61366 at 60iterations 0.3871109 7.573883 at 70iterations 0.2189744 4.114105 at 80iterations 0.1236692 2.518902 at 90iterations 7.0006721E-02 1.263805 at 100iterations 3.9573662E-02 0.7575401 at 110iterations 2.2414956E-02 0.3928452 at 120iterations 1.2788840E-02 0.2294579 at 130iterations 7.3747593E-03 0.1257782 at 140iterations 4.3602353E-03 8.1474304E-02 at 150iterations 2.6883970E-03 4.7576904E-02 at 160iterations 1.7646790E-03 3.2092094E-02 at 170iterations 1.2476502E-03 2.1575928E-02 at 180iterations finished qdiffx linear iterations at : 16:04:51 total time elapsed so far: 16.54000 # loops : 180 mean,max change (kT/e) : 1.2476502E-03 2.1575928E-02 energy calculations done at 16.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.72000 DelPhi exited at 16:04:52 16.723u 0.329s 0:17.66 96.4% 0+0k 0+0io 0pf+0w