Tue Oct 11 06:31:18 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 Tue Oct 11 2011 at 06:31:18 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7052298 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): -20.68800 23.71200 ymin,ymax (A): -28.67600 11.04000 zmin,zma (A): -13.75200 36.72800 x,y,z range (A): 44.40000 39.71600 50.48000 scale (grids/A): 0.7052298 object centre (A): 1.512000 -8.817999 11.48800 number of atom coordinates read : 2010 total number of charged atoms : 1915 net assigned charge : 6.931010 assigned positive charge : 310.1871 centred at (gu) : 90.41022 90.61874 89.49932 assigned negative charge : -303.2562 centred at (gu) : 90.22240 90.59592 89.47761 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6805 nv = 96 ne = 84 npr = 39744 no. pairs analyzed = 39744 no. exposed pairs = 2460 no. arc points = 16934 no. surface atoms = 840 nbur = 1170 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 479 mr = 3930 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3292 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1654 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7680 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9610058E-08 5.9162399E-08 midg,1,midg; midg,igrid,midg 3.9851326E-08 7.3783781E-08 1,midg,midg; igrid,midg,midg -2.9582765E-08 1.5111958E-07 gauss-seidel spectral radius is 0.9895137 estimated iterations to convergence 80 setup time was (sec) 0.5200000 now iterating at: 06:31:19 rms-change max change #iterations 0.1957328 28.59006 at 10iterations 2.3928603E-02 3.687284 at 20iterations 3.0889302E-03 0.3700743 at 30iterations 4.6203038E-04 7.3211670E-02 at 40iterations 9.0502654E-05 1.3027191E-02 at 50iterations finished qdiffx linear iterations at : 06:31:23 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 9.0502654E-05 1.3027191E-02 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 06:31:23 4.356u 0.389s 0:05.29 89.4% 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 Tue Oct 11 2011 at 06:31:23 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.115690 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): -20.68800 23.71200 ymin,ymax (A): -28.67600 11.04000 zmin,zma (A): -13.75200 36.72800 x,y,z range (A): 44.40000 39.71600 50.48000 scale (grids/A): 2.115690 object centre (A): 1.512000 -8.817999 11.48800 number of atom coordinates read : 2010 total number of charged atoms : 1915 net assigned charge : 6.931010 assigned positive charge : 310.1871 centred at (gu) : 91.23048 91.85663 88.49775 assigned negative charge : -303.2562 centred at (gu) : 90.66730 91.78784 88.43298 start vw surface at 0.1000000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 72440 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16934 grid for indexing accessible points = 1.400000 m= 29024 mr = 51384 m= 5655 mr = 22048 m= 558 mr = 3744 m= 10 mr = 278 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 0.6000000 number of dielectric boundary points 30233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15210 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) : 0.7052298 object centre at (A) : 1.512000 -8.817999 11.48800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8438061E-02 4.2647630E-02 midg,1,midg; midg,igrid,midg 1.6467144E-03 3.3839852E-02 1,midg,midg; igrid,midg,midg 1.3648623E-02 4.5295343E-02 gauss-seidel spectral radius is 0.9988197 estimated iterations to convergence 230 setup time was (sec) 0.9500000 now iterating at: 06:31:25 rms-change max change #iterations 4.501632 166.6292 at 10iterations 2.223008 82.22027 at 20iterations 1.098986 38.40298 at 30iterations 0.5425014 16.59836 at 40iterations 0.2686925 8.109859 at 50iterations 0.1333114 4.087839 at 60iterations 6.5739177E-02 2.238168 at 70iterations 3.2855332E-02 1.016937 at 80iterations 1.6251620E-02 0.5388412 at 90iterations 8.1096049E-03 0.2495651 at 100iterations 4.0546320E-03 0.1240997 at 110iterations 2.0436666E-03 6.1124802E-02 at 120iterations finished qdiffx linear iterations at : 06:31:34 total time elapsed so far: 10.52000 # loops : 120 mean,max change (kT/e) : 2.0436666E-03 6.1124802E-02 energy calculations done at 10.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.68000 DelPhi exited at 06:31:35 10.689u 0.458s 0:11.70 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 06:31:35 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.173534 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): -20.68800 23.71200 ymin,ymax (A): -28.67600 11.04000 zmin,zma (A): -13.75200 36.72800 x,y,z range (A): 44.40000 39.71600 50.48000 scale (grids/A): 3.173534 object centre (A): 1.512000 -8.817999 11.48800 number of atom coordinates read : 2010 total number of charged atoms : 1915 net assigned charge : 6.931010 assigned positive charge : 310.1871 centred at (gu) : 91.84574 92.78494 87.74673 assigned negative charge : -303.2562 centred at (gu) : 91.00110 92.68180 87.64950 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 167069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16934 grid for indexing accessible points = 1.400000 m= 90384 mr = 123692 m= 36794 mr = 75211 m= 10570 mr = 30224 m= 2128 mr = 8187 m= 234 mr = 1546 m= 6 mr = 147 m= 0 mr = 2 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.880000 number of dielectric boundary points 68176 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 15320 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) : 2.115690 object centre at (A) : 1.512000 -8.817999 11.48800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7182047 0.3284858 midg,1,midg; midg,igrid,midg -1.7948573E-02 0.2720837 1,midg,midg; igrid,midg,midg 0.2400505 0.3626459 gauss-seidel spectral radius is 0.9992912 estimated iterations to convergence 296 setup time was (sec) 2.220000 now iterating at: 06:31:38 rms-change max change #iterations 10.07241 441.0823 at 10iterations 5.940330 118.7768 at 20iterations 3.504011 80.77174 at 30iterations 2.062251 44.86395 at 40iterations 1.210325 21.83314 at 50iterations 0.7110528 13.89932 at 60iterations 0.4164653 7.515335 at 70iterations 0.2440383 4.450848 at 80iterations 0.1426481 2.531291 at 90iterations 8.3457209E-02 1.739269 at 100iterations 4.9103450E-02 0.8650360 at 110iterations 2.8948640E-02 0.5624695 at 120iterations 1.7191235E-02 0.3287964 at 130iterations 1.0379441E-02 0.2100372 at 140iterations 6.4203176E-03 0.1312943 at 150iterations 4.1288319E-03 8.3648682E-02 at 160iterations 2.8061499E-03 5.6022644E-02 at 170iterations 2.0063836E-03 3.9928436E-02 at 180iterations finished qdiffx linear iterations at : 06:31:54 total time elapsed so far: 18.27000 # loops : 180 mean,max change (kT/e) : 2.0063836E-03 3.9928436E-02 energy calculations done at 18.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.43000 DelPhi exited at 06:31:55 18.434u 0.487s 0:19.61 96.4% 0+0k 0+0io 0pf+0w