Tue Oct 11 03:56:11 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 Tue Oct 11 2011 at 03:56:11 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2388 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6742935 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): -6.639000 37.36800 ymin,ymax (A): -26.95600 17.57500 zmin,zma (A): -7.683000 45.11300 x,y,z range (A): 44.00700 44.53100 52.79600 scale (grids/A): 0.6742935 object centre (A): 15.36450 -4.690499 18.71500 number of atom coordinates read : 2388 total number of charged atoms : 2243 net assigned charge : 7.162014 assigned positive charge : 354.6152 centred at (gu) : 89.53098 90.41370 90.86382 assigned negative charge : -347.4537 centred at (gu) : 89.34385 90.15804 90.77771 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7260 nv = 96 ne = 84 npr = 49382 no. pairs analyzed = 49382 no. exposed pairs = 2851 no. arc points = 20051 no. surface atoms = 967 nbur = 1421 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 4084 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.2800000 number of dielectric boundary points 3532 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1967 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8457 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9410795E-09 5.7289572E-08 midg,1,midg; midg,igrid,midg -3.6648959E-08 9.7472160E-08 1,midg,midg; igrid,midg,midg -2.4319490E-08 6.6319330E-08 gauss-seidel spectral radius is 0.9885752 estimated iterations to convergence 76 setup time was (sec) 0.5500000 now iterating at: 03:56:12 rms-change max change #iterations 0.1698441 25.67278 at 10iterations 1.9212985E-02 2.539486 at 20iterations 2.1468112E-03 0.2787371 at 30iterations 2.4317465E-04 3.0301571E-02 at 40iterations 2.9838115E-05 3.9710999E-03 at 50iterations finished qdiffx linear iterations at : 03:56:16 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 2.9838115E-05 3.9710999E-03 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 03:56:17 4.412u 0.384s 0:05.56 86.1% 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 Tue Oct 11 2011 at 03:56:17 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2388 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.022881 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): -6.639000 37.36800 ymin,ymax (A): -26.95600 17.57500 zmin,zma (A): -7.683000 45.11300 x,y,z range (A): 44.00700 44.53100 52.79600 scale (grids/A): 2.022881 object centre (A): 15.36450 -4.690499 18.71500 number of atom coordinates read : 2388 total number of charged atoms : 2243 net assigned charge : 7.162014 assigned positive charge : 354.6152 centred at (gu) : 88.59233 91.24081 92.59102 assigned negative charge : -347.4537 centred at (gu) : 88.03130 90.47382 92.33302 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20051 grid for indexing accessible points = 1.400000 m= 29905 mr = 54480 m= 5222 mr = 22493 m= 371 mr = 3451 m= 6 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 793 time to turn everything in is 0.6400000 number of dielectric boundary points 32252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17783 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) : 0.6742935 object centre at (A) : 15.36450 -4.690499 18.71500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2949774E-02 1.9965913E-02 midg,1,midg; midg,igrid,midg -7.9772156E-03 6.1647594E-02 1,midg,midg; igrid,midg,midg 9.4562853E-03 5.4539278E-02 gauss-seidel spectral radius is 0.9987597 estimated iterations to convergence 225 setup time was (sec) 0.9200000 now iterating at: 03:56:18 rms-change max change #iterations 4.434312 197.8494 at 10iterations 2.160236 83.35596 at 20iterations 1.045990 41.67938 at 30iterations 0.5081261 15.69067 at 40iterations 0.2466007 7.637299 at 50iterations 0.1201938 4.604832 at 60iterations 5.8291316E-02 1.722477 at 70iterations 2.8333390E-02 0.8541155 at 80iterations 1.3780949E-02 0.4364367 at 90iterations 6.7008222E-03 0.2157822 at 100iterations 3.2497786E-03 9.7008467E-02 at 110iterations 1.5800976E-03 4.6056747E-02 at 120iterations finished qdiffx linear iterations at : 03:56:28 total time elapsed so far: 10.47000 # loops : 120 mean,max change (kT/e) : 1.5800976E-03 4.6056747E-02 energy calculations done at 10.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.63000 DelPhi exited at 03:56:29 10.634u 0.454s 0:11.64 95.1% 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 Tue Oct 11 2011 at 03:56:29 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2388 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 3.034321 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): -6.639000 37.36800 ymin,ymax (A): -26.95600 17.57500 zmin,zma (A): -7.683000 45.11300 x,y,z range (A): 44.00700 44.53100 52.79600 scale (grids/A): 3.034321 object centre (A): 15.36450 -4.690499 18.71500 number of atom coordinates read : 2388 total number of charged atoms : 2243 net assigned charge : 7.162014 assigned positive charge : 354.6152 centred at (gu) : 87.88860 91.86104 93.88646 assigned negative charge : -347.4537 centred at (gu) : 87.04685 90.71075 93.49941 start vw surface at 0.1100000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 178110 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20051 grid for indexing accessible points = 1.400000 m= 94481 mr = 131030 m= 36935 mr = 78464 m= 9545 mr = 30030 m= 1560 mr = 7333 m= 136 mr = 1067 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 2615 time to turn everything in is 1.690000 number of dielectric boundary points 72787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 17928 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) : 2.022881 object centre at (A) : 15.36450 -4.690499 18.71500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1582360 0.4384639 midg,1,midg; midg,igrid,midg -0.1017701 0.4952649 1,midg,midg; igrid,midg,midg 6.8330385E-02 0.4444869 gauss-seidel spectral radius is 0.9992818 estimated iterations to convergence 294 setup time was (sec) 2.020000 now iterating at: 03:56:31 rms-change max change #iterations 10.20429 490.0028 at 10iterations 5.973136 133.1884 at 20iterations 3.501495 65.46277 at 30iterations 2.044709 39.07517 at 40iterations 1.193447 20.93947 at 50iterations 0.6942938 12.93781 at 60iterations 0.4045900 7.935522 at 70iterations 0.2352120 4.361694 at 80iterations 0.1364556 2.375777 at 90iterations 7.9158947E-02 1.369846 at 100iterations 4.5987256E-02 0.7734528 at 110iterations 2.6733201E-02 0.4713745 at 120iterations 1.5569623E-02 0.2723007 at 130iterations 9.0235760E-03 0.1729469 at 140iterations 5.2493853E-03 8.7680817E-02 at 150iterations 3.0568028E-03 5.0079346E-02 at 160iterations 1.7856023E-03 3.2537460E-02 at 170iterations 1.0475992E-03 1.8082619E-02 at 180iterations finished qdiffx linear iterations at : 03:56:47 total time elapsed so far: 17.83000 # loops : 180 mean,max change (kT/e) : 1.0475992E-03 1.8082619E-02 energy calculations done at 17.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.00000 DelPhi exited at 03:56:48 18.004u 0.451s 0:18.88 97.7% 0+0k 0+0io 0pf+0w