Sun Oct 9 14:16:12 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 14:16:13 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2702 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5721265 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): 2.6999950E-02 52.11900 ymin,ymax (A): -9.943000 39.95800 zmin,zma (A): -15.37000 46.85400 x,y,z range (A): 52.09200 49.90100 62.22400 scale (grids/A): 0.5721265 object centre (A): 26.07300 15.00750 15.74200 number of atom coordinates read : 2702 total number of charged atoms : 2556 net assigned charge : 6.445022 assigned positive charge : 410.9395 centred at (gu) : 89.63041 90.49996 88.43796 assigned negative charge : -404.4955 centred at (gu) : 89.59384 90.39160 88.47103 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5826 nv = 96 ne = 84 npr = 53129 no. pairs analyzed = 53129 no. exposed pairs = 3550 no. arc points = 24948 no. surface atoms = 1195 nbur = 1507 mkacc time = 0.1200000 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 = 1.512000 m= 264 mr = 2907 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2588 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7443 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2455298E-09 3.8493286E-10 midg,1,midg; midg,igrid,midg -5.5707827E-10 3.0281542E-09 1,midg,midg; igrid,midg,midg 5.2608307E-10 1.4746957E-09 gauss-seidel spectral radius is 0.9842163 estimated iterations to convergence 65 setup time was (sec) 0.5300000 now iterating at: 14:16:13 rms-change max change #iterations 8.8910811E-02 14.88051 at 10iterations 6.8679242E-03 1.173794 at 20iterations 5.4415909E-04 9.3278885E-02 at 30iterations 6.2483268E-05 1.1207581E-02 at 40iterations 1.1494096E-05 1.8196106E-03 at 50iterations finished qdiffx linear iterations at : 14:16:16 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.1494096E-05 1.8196106E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 14:16:16 3.480u 0.183s 0:03.94 92.8% 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 Sun Oct 9 2011 at 14:16:17 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2702 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 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: 1.716380 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): 2.6999950E-02 52.11900 ymin,ymax (A): -9.943000 39.95800 zmin,zma (A): -15.37000 46.85400 x,y,z range (A): 52.09200 49.90100 62.22400 scale (grids/A): 1.716380 object centre (A): 26.07300 15.00750 15.74200 number of atom coordinates read : 2702 total number of charged atoms : 2556 net assigned charge : 6.445022 assigned positive charge : 410.9395 centred at (gu) : 88.89062 91.49939 85.31307 assigned negative charge : -404.4955 centred at (gu) : 88.78117 91.17479 85.41299 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24948 grid for indexing accessible points = 1.400000 m= 20320 mr = 42208 m= 2327 mr = 13669 m= 92 mr = 1134 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 29227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 290 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 19791 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) : 0.5721265 object centre at (A) : 26.07300 15.00750 15.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5077223E-02 1.1012253E-02 midg,1,midg; midg,igrid,midg -1.5549907E-03 5.0258893E-03 1,midg,midg; igrid,midg,midg -1.0625141E-02 -3.5636805E-04 gauss-seidel spectral radius is 0.9983430 estimated iterations to convergence 195 setup time was (sec) 0.7500000 now iterating at: 14:16:17 rms-change max change #iterations 3.546729 176.5192 at 10iterations 1.529523 52.50626 at 20iterations 0.6641011 24.81120 at 30iterations 0.2876571 11.43059 at 40iterations 0.1244102 4.396246 at 50iterations 5.4024372E-02 1.832680 at 60iterations 2.3388857E-02 0.8297749 at 70iterations 1.0167787E-02 0.3666611 at 80iterations 4.4292812E-03 0.1486664 at 90iterations 1.9248768E-03 6.3644409E-02 at 100iterations 8.4185123E-04 2.8442383E-02 at 110iterations 3.7045762E-04 1.3504982E-02 at 120iterations finished qdiffx linear iterations at : 14:16:24 total time elapsed so far: 7.110000 # loops : 120 mean,max change (kT/e) : 3.7045762E-04 1.3504982E-02 energy calculations done at 7.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 14:16:24 7.289u 0.202s 0:07.81 95.7% 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 14:16:24 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2702 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 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: 2.574569 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): 2.6999950E-02 52.11900 ymin,ymax (A): -9.943000 39.95800 zmin,zma (A): -15.37000 46.85400 x,y,z range (A): 52.09200 49.90100 62.22400 scale (grids/A): 2.574569 object centre (A): 26.07300 15.00750 15.74200 number of atom coordinates read : 2702 total number of charged atoms : 2556 net assigned charge : 6.445022 assigned positive charge : 410.9395 centred at (gu) : 88.33563 92.24890 82.96946 assigned negative charge : -404.4955 centred at (gu) : 88.17167 91.76196 83.11934 start vw surface at 0.1400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 147459 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24948 grid for indexing accessible points = 1.400000 m= 68645 mr = 103661 m= 20818 mr = 53419 m= 3753 mr = 15497 m= 363 mr = 2350 m= 11 mr = 159 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 65963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 20431 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) : 1.716380 object centre at (A) : 26.07300 15.00750 15.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.025385 0.1642092 midg,1,midg; midg,igrid,midg -3.3103533E-02 1.3962828E-02 1,midg,midg; igrid,midg,midg -0.1237536 -8.9358278E-03 gauss-seidel spectral radius is 0.9991826 estimated iterations to convergence 276 setup time was (sec) 1.420000 now iterating at: 14:16:26 rms-change max change #iterations 8.955029 263.3878 at 10iterations 5.171522 128.9316 at 20iterations 2.962341 78.32008 at 30iterations 1.682676 36.85859 at 40iterations 0.9562471 22.22380 at 50iterations 0.5391177 12.88804 at 60iterations 0.3043378 6.165206 at 70iterations 0.1707425 3.798050 at 80iterations 9.5946528E-02 1.955362 at 90iterations 5.3845212E-02 1.230737 at 100iterations 3.0277118E-02 0.6496887 at 110iterations 1.6960189E-02 0.3554488 at 120iterations 9.5158443E-03 0.2002325 at 130iterations 5.3390232E-03 0.1126556 at 140iterations 3.0064972E-03 6.3980103E-02 at 150iterations 1.6975077E-03 3.4790039E-02 at 160iterations 9.6246839E-04 2.2766113E-02 at 170iterations 5.5019441E-04 1.1291504E-02 at 180iterations finished qdiffx linear iterations at : 14:16:36 total time elapsed so far: 11.67000 # loops : 180 mean,max change (kT/e) : 5.5019441E-04 1.1291504E-02 energy calculations done at 11.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.84000 DelPhi exited at 14:16:37 11.847u 0.211s 0:12.35 97.5% 0+0k 0+0io 0pf+0w