Wed Feb 15 08:55:42 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:42 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 ! Automatically converted by prot2crg.py # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3686 !!! WARNING: HEM 900 has a net charge of -2.0000 !!! WARNING: ZN 951 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5559980 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): -30.10400 33.92500 ymin,ymax (A): -31.44200 31.33500 zmin,zma (A): 29.24300 86.38400 x,y,z range (A): 64.02901 62.77700 57.14100 scale (grids/A): 0.5559980 object centre (A): 1.910501 -5.3500175E-02 57.81350 number of atom coordinates read : 3686 total number of charged atoms : 3534 net assigned charge : -5.999985 assigned positive charge : 558.0215 centred at (gu) : 90.00353 91.66523 91.18910 assigned negative charge : -564.0234 centred at (gu) : 90.08995 91.72526 91.14634 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7255 nv = 96 ne = 84 npr = 76412 no. pairs analyzed = 76412 no. exposed pairs = 4724 no. arc points = 33156 no. surface atoms = 1565 nbur = 2121 mkacc time = 0.1800000 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 = 1.540000 m= 282 mr = 3680 m= 1 mr = 22 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 0.4200000 number of dielectric boundary points 3836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3324 ## 377 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9587 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.9707962E-10 -2.1412906E-11 midg,1,midg; midg,igrid,midg 1.1471736E-10 -1.9138602E-09 1,midg,midg; igrid,midg,midg 4.9674798E-10 -1.5993131E-09 gauss-seidel spectral radius is 0.9833686 estimated iterations to convergence 64 setup time was (sec) 0.6400000 now iterating at: 08:55:43 rms-change max change #iterations 8.9349456E-02 13.43977 at 10iterations 6.2747002E-03 0.8569946 at 20iterations 4.9069780E-04 7.5740814E-02 at 30iterations 6.6957189E-05 1.0138035E-02 at 40iterations 1.6488440E-05 2.7461052E-03 at 50iterations finished qdiffx linear iterations at : 08:55:45 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.6488440E-05 2.7461052E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 08:55:47 3.508u 0.188s 0:05.33 69.0% 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 Wed Feb 15 2012 at 08:55:47 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 ! Automatically converted by prot2crg.py # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3686 !!! WARNING: HEM 900 has a net charge of -2.0000 !!! WARNING: ZN 951 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.667994 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): -30.10400 33.92500 ymin,ymax (A): -31.44200 31.33500 zmin,zma (A): 29.24300 86.38400 x,y,z range (A): 64.02901 62.77700 57.14100 scale (grids/A): 1.667994 object centre (A): 1.910501 -5.3500175E-02 57.81350 number of atom coordinates read : 3686 total number of charged atoms : 3534 net assigned charge : -5.999985 assigned positive charge : 558.0215 centred at (gu) : 90.00948 94.99462 93.56631 assigned negative charge : -564.0234 centred at (gu) : 90.26952 95.17494 93.43865 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 79988 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33156 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24382 mr = 53980 m= 2653 mr = 16481 m= 94 mr = 1280 m= 0 mr = 10 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 287 time to turn everything in is 0.6200000 number of dielectric boundary points 35366 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 348 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 27271 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) : 0.5559980 object centre at (A) : 1.910501 -5.3500175E-02 57.81350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4088586E-03 -7.7028447E-03 midg,1,midg; midg,igrid,midg -1.0019651E-02 -2.1257609E-02 1,midg,midg; igrid,midg,midg 9.6402727E-03 -9.8330062E-03 gauss-seidel spectral radius is 0.9983301 estimated iterations to convergence 194 setup time was (sec) 0.9400000 now iterating at: 08:55:48 rms-change max change #iterations 3.996974 154.8270 at 10iterations 1.717755 66.26095 at 20iterations 0.7436655 26.77981 at 30iterations 0.3195229 11.09437 at 40iterations 0.1378715 4.571724 at 50iterations 5.9878998E-02 1.887928 at 60iterations 2.5826389E-02 0.8544540 at 70iterations 1.1180224E-02 0.3642621 at 80iterations 4.8341495E-03 0.1539873 at 90iterations 2.0954935E-03 7.3636055E-02 at 100iterations 9.1186026E-04 3.0075073E-02 at 110iterations 3.9984600E-04 1.3511658E-02 at 120iterations finished qdiffx linear iterations at : 08:55:55 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 3.9984600E-04 1.3511658E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 08:55:56 8.009u 0.182s 0:08.81 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 Wed Feb 15 2012 at 08:55:56 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 ! Automatically converted by prot2crg.py # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3686 !!! WARNING: HEM 900 has a net charge of -2.0000 !!! WARNING: ZN 951 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.501991 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): -30.10400 33.92500 ymin,ymax (A): -31.44200 31.33500 zmin,zma (A): 29.24300 86.38400 x,y,z range (A): 64.02901 62.77700 57.14100 scale (grids/A): 2.501991 object centre (A): 1.910501 -5.3500175E-02 57.81350 number of atom coordinates read : 3686 total number of charged atoms : 3534 net assigned charge : -5.999985 assigned positive charge : 558.0215 centred at (gu) : 90.01405 97.49158 95.34910 assigned negative charge : -564.0234 centred at (gu) : 90.40403 97.76244 95.15788 start vw surface at 0.1900000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 185730 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33156 grid for indexing accessible points = 1.400000 m= 84759 mr = 132205 m= 23727 mr = 66397 m= 4139 mr = 17501 m= 388 mr = 2689 m= 5 mr = 185 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 1085 time to turn everything in is 1.530000 number of dielectric boundary points 79771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 28250 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) : 1.667994 object centre at (A) : 1.910501 -5.3500175E-02 57.81350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1158768 -3.5499249E-02 midg,1,midg; midg,igrid,midg -0.3303851 -0.3075527 1,midg,midg; igrid,midg,midg 0.1191776 -3.8529973E-02 gauss-seidel spectral radius is 0.9991963 estimated iterations to convergence 279 setup time was (sec) 1.860000 now iterating at: 08:55:58 rms-change max change #iterations 10.13373 325.9260 at 10iterations 5.807502 130.7475 at 20iterations 3.303321 70.61209 at 30iterations 1.881637 40.70080 at 40iterations 1.065537 22.73639 at 50iterations 0.6018232 14.41593 at 60iterations 0.3395496 7.842216 at 70iterations 0.1913742 4.408719 at 80iterations 0.1081988 2.389908 at 90iterations 6.0818933E-02 1.198318 at 100iterations 3.4205470E-02 0.6542425 at 110iterations 1.9250469E-02 0.3819294 at 120iterations 1.0794827E-02 0.2234631 at 130iterations 6.0799429E-03 0.1223354 at 140iterations 3.4041090E-03 6.6191196E-02 at 150iterations 1.9124384E-03 3.8002014E-02 at 160iterations 1.0743896E-03 2.0908356E-02 at 170iterations 6.0316431E-04 1.1821747E-02 at 180iterations finished qdiffx linear iterations at : 08:56:11 total time elapsed so far: 14.92000 # loops : 180 mean,max change (kT/e) : 6.0316431E-04 1.1821747E-02 energy calculations done at 14.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.11000 DelPhi exited at 08:56:12 15.114u 0.216s 0:15.90 96.3% 0+0k 0+0io 0pf+0w