Tue Oct 11 08:33:56 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 08:33:56 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2044 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: 0.7528496 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): -2.840000 44.44700 ymin,ymax (A): 6.789999 54.02400 zmin,zma (A): -13.52800 29.13200 x,y,z range (A): 47.28700 47.23400 42.66000 scale (grids/A): 0.7528496 object centre (A): 20.80350 30.40700 7.802000 number of atom coordinates read : 2044 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 90.68927 91.11301 90.19708 assigned negative charge : -302.7272 centred at (gu) : 90.56845 90.99462 90.25260 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8092 nv = 96 ne = 84 npr = 40539 no. pairs analyzed = 40539 no. exposed pairs = 2513 no. arc points = 17216 no. surface atoms = 855 nbur = 1189 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 643 mr = 4766 m= 4 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1456 ## 131 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 8370 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3119735E-07 1.0506921E-07 midg,1,midg; midg,igrid,midg 1.9917826E-08 3.8821946E-07 1,midg,midg; igrid,midg,midg 1.8083748E-08 3.6236062E-07 gauss-seidel spectral radius is 0.9907930 estimated iterations to convergence 85 setup time was (sec) 0.4800000 now iterating at: 08:33:56 rms-change max change #iterations 0.2543044 34.46813 at 10iterations 3.6443621E-02 5.567688 at 20iterations 5.2388641E-03 0.6410205 at 30iterations 8.5649133E-04 0.1081772 at 40iterations 1.9446222E-04 2.2817612E-02 at 50iterations finished qdiffx linear iterations at : 08:33:59 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.9446222E-04 2.2817612E-02 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 08:34:00 3.339u 0.196s 0:04.19 84.0% 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 Tue Oct 11 2011 at 08:34:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2044 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.258549 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): -2.840000 44.44700 ymin,ymax (A): 6.789999 54.02400 zmin,zma (A): -13.52800 29.13200 x,y,z range (A): 47.28700 47.23400 42.66000 scale (grids/A): 2.258549 object centre (A): 20.80350 30.40700 7.802000 number of atom coordinates read : 2044 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 92.06781 93.33916 90.59138 assigned negative charge : -302.7272 centred at (gu) : 91.70527 92.98396 90.75784 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84839 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17216 grid for indexing accessible points = 1.400000 m= 37179 mr = 60808 m= 8426 mr = 29027 m= 966 mr = 5958 m= 36 mr = 545 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 35108 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15302 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) : 0.7528496 object centre at (A) : 20.80350 30.40700 7.802000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8866759E-02 3.3463176E-02 midg,1,midg; midg,igrid,midg -4.0397573E-02 5.1564880E-02 1,midg,midg; igrid,midg,midg 5.9876699E-02 0.1133612 gauss-seidel spectral radius is 0.9989462 estimated iterations to convergence 244 setup time was (sec) 0.9500000 now iterating at: 08:34:01 rms-change max change #iterations 5.044771 180.3815 at 10iterations 2.595115 74.60936 at 20iterations 1.332757 38.38298 at 30iterations 0.6870497 19.42657 at 40iterations 0.3537937 9.768193 at 50iterations 0.1819993 5.110513 at 60iterations 9.3768381E-02 2.611938 at 70iterations 4.8204619E-02 1.393799 at 80iterations 2.4812670E-02 0.6582680 at 90iterations 1.2866087E-02 0.3914280 at 100iterations 6.6762976E-03 0.1733189 at 110iterations 3.4960839E-03 9.5169067E-02 at 120iterations finished qdiffx linear iterations at : 08:34:09 total time elapsed so far: 8.890000 # loops : 120 mean,max change (kT/e) : 3.4960839E-03 9.5169067E-02 energy calculations done at 8.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.060000 DelPhi exited at 08:34:10 9.062u 0.221s 0:09.63 96.3% 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 08:34:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2044 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: 3.387823 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): -2.840000 44.44700 ymin,ymax (A): 6.789999 54.02400 zmin,zma (A): -13.52800 29.13200 x,y,z range (A): 47.28700 47.23400 42.66000 scale (grids/A): 3.387823 object centre (A): 20.80350 30.40700 7.802000 number of atom coordinates read : 2044 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 93.10163 95.00874 90.88707 assigned negative charge : -302.7272 centred at (gu) : 92.55800 94.47598 91.13686 start vw surface at 0.1300000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 194758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17216 grid for indexing accessible points = 1.400000 m= 111408 mr = 145629 m= 50699 mr = 93794 m= 16715 mr = 42746 m= 3856 mr = 13466 m= 553 mr = 2907 m= 33 mr = 363 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.020000 number of dielectric boundary points 79115 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 15367 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) : 2.258549 object centre at (A) : 20.80350 30.40700 7.802000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1198983 0.2585604 midg,1,midg; midg,igrid,midg -0.4771140 0.4387043 1,midg,midg; igrid,midg,midg 0.3803122 0.7273699 gauss-seidel spectral radius is 0.9993281 estimated iterations to convergence 304 setup time was (sec) 2.320000 now iterating at: 08:34:12 rms-change max change #iterations 10.84359 295.4692 at 10iterations 6.526618 173.2038 at 20iterations 3.898041 80.58752 at 30iterations 2.329297 43.91895 at 40iterations 1.388141 27.12765 at 50iterations 0.8250563 14.92638 at 60iterations 0.4910548 8.420109 at 70iterations 0.2926645 5.210796 at 80iterations 0.1737108 2.911703 at 90iterations 0.1028091 1.640466 at 100iterations 6.1130852E-02 1.081774 at 110iterations 3.6472917E-02 0.5952301 at 120iterations 2.1902505E-02 0.3680763 at 130iterations 1.3286334E-02 0.2159929 at 140iterations 8.2285544E-03 0.1405678 at 150iterations 5.2936915E-03 9.7787857E-02 at 160iterations 3.5699192E-03 5.6377411E-02 at 170iterations 2.5649250E-03 4.6432495E-02 at 180iterations finished qdiffx linear iterations at : 08:34:23 total time elapsed so far: 13.22000 # loops : 180 mean,max change (kT/e) : 2.5649250E-03 4.6432495E-02 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.41000 DelPhi exited at 08:34:24 13.416u 0.253s 0:14.27 95.7% 0+0k 0+0io 0pf+0w