Sun Oct 9 04:11:12 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+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 Sun Oct 9 2011 at 04:11:12 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4848 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 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: 0.4181201 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): -2.552000 78.88100 ymin,ymax (A): -12.41400 55.74700 zmin,zma (A): -16.72600 68.41700 x,y,z range (A): 81.43301 68.16100 85.14300 scale (grids/A): 0.4181201 object centre (A): 38.16450 21.66650 25.84550 number of atom coordinates read : 4848 total number of charged atoms : 4530 net assigned charge : 23.29997 assigned positive charge : 709.9575 centred at (gu) : 85.55214 91.72250 83.64307 assigned negative charge : -686.6625 centred at (gu) : 85.40125 91.76823 83.50829 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4910 nv = 96 ne = 84 npr = 98371 no. pairs analyzed = 98371 no. exposed pairs = 6356 no. arc points = 44279 no. surface atoms = 2121 nbur = 2727 mkacc time = 0.1700000 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 = 1.988000 m= 106 mr = 2143 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 2873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3294 ## 721 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6614 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5927251E-12 6.6955035E-13 midg,1,midg; midg,igrid,midg 1.8146990E-12 2.4992888E-12 1,midg,midg; igrid,midg,midg -2.4415682E-12 1.2484186E-12 gauss-seidel spectral radius is 0.9708772 estimated iterations to convergence 49 setup time was (sec) 0.5100000 now iterating at: 04:11:13 rms-change max change #iterations 2.4645716E-02 4.882063 at 10iterations 2.7841637E-03 0.4845200 at 20iterations 7.9988549E-04 0.1324596 at 30iterations 2.3673543E-04 3.9323807E-02 at 40iterations 7.0231705E-05 1.1680603E-02 at 50iterations finished qdiffx linear iterations at : 04:11:16 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 7.0231705E-05 1.1680603E-02 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 04:11:16 3.625u 0.173s 0:04.17 90.8% 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 04:11:16 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4848 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 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: 1.254360 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): -2.552000 78.88100 ymin,ymax (A): -12.41400 55.74700 zmin,zma (A): -16.72600 68.41700 x,y,z range (A): 81.43301 68.16100 85.14300 scale (grids/A): 1.254360 object centre (A): 38.16450 21.66650 25.84550 number of atom coordinates read : 4848 total number of charged atoms : 4530 net assigned charge : 23.29997 assigned positive charge : 709.9575 centred at (gu) : 76.65474 95.16568 70.92751 assigned negative charge : -686.6625 centred at (gu) : 76.20295 95.30428 70.52478 start vw surface at 0.1100000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 57625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44279 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.876000 m= 11992 mr = 36214 m= 489 mr = 6764 m= 4 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 740 time to turn everything in is 0.3100000 number of dielectric boundary points 27046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 792 ## 26 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 30967 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) : 0.4181201 object centre at (A) : 38.16450 21.66650 25.84550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0988334E-02 2.2138723E-03 midg,1,midg; midg,igrid,midg 2.8451150E-03 2.2533161E-03 1,midg,midg; igrid,midg,midg -2.0510664E-04 1.5022883E-03 gauss-seidel spectral radius is 0.9969604 estimated iterations to convergence 145 setup time was (sec) 0.5200000 now iterating at: 04:11:17 rms-change max change #iterations 2.237649 115.5509 at 10iterations 0.7167137 30.81956 at 20iterations 0.2315270 9.729761 at 30iterations 7.5565770E-02 3.568610 at 40iterations 2.5233490E-02 1.048733 at 50iterations 9.0008434E-03 0.3539600 at 60iterations 3.8702930E-03 0.1563463 at 70iterations 2.0898094E-03 7.5920105E-02 at 80iterations 1.2747614E-03 4.1836977E-02 at 90iterations 8.1696035E-04 2.7133942E-02 at 100iterations 5.2975770E-04 1.6853333E-02 at 110iterations 3.4505228E-04 1.0887146E-02 at 120iterations finished qdiffx linear iterations at : 04:11:24 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 3.4505228E-04 1.0887146E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 04:11:24 7.625u 0.225s 0:08.16 96.0% 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 Sun Oct 9 2011 at 04:11:24 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4848 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 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: 1.881541 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): -2.552000 78.88100 ymin,ymax (A): -12.41400 55.74700 zmin,zma (A): -16.72600 68.41700 x,y,z range (A): 81.43301 68.16100 85.14300 scale (grids/A): 1.881541 object centre (A): 38.16450 21.66650 25.84550 number of atom coordinates read : 4848 total number of charged atoms : 4530 net assigned charge : 23.29997 assigned positive charge : 709.9575 centred at (gu) : 69.98161 97.74805 61.39099 assigned negative charge : -686.6625 centred at (gu) : 69.30441 97.95637 60.78704 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 135466 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44279 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 47723 mr = 90899 m= 7550 mr = 34404 m= 433 mr = 4602 m= 9 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2399 time to turn everything in is 0.7100000 number of dielectric boundary points 61126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 35640 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) : 1.254360 object centre at (A) : 38.16450 21.66650 25.84550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3392190 2.9153503E-02 midg,1,midg; midg,igrid,midg 6.8080634E-02 4.2834900E-02 1,midg,midg; igrid,midg,midg 9.2856111E-03 2.1658806E-02 gauss-seidel spectral radius is 0.9986874 estimated iterations to convergence 219 setup time was (sec) 0.9300000 now iterating at: 04:11:25 rms-change max change #iterations 6.891627 222.2749 at 10iterations 3.414329 109.6811 at 20iterations 1.670033 49.87019 at 30iterations 0.8133883 20.83216 at 40iterations 0.3941806 12.40498 at 50iterations 0.1905627 6.062466 at 60iterations 9.1997735E-02 2.429035 at 70iterations 4.4409983E-02 1.217185 at 80iterations 2.1380024E-02 0.5253601 at 90iterations 1.0385070E-02 0.2681742 at 100iterations 5.1128566E-03 0.1272354 at 110iterations 2.5994284E-03 6.8359375E-02 at 120iterations 1.3932794E-03 3.5678864E-02 at 130iterations 8.1060984E-04 2.0431519E-02 at 140iterations 5.1547622E-04 1.2500763E-02 at 150iterations 3.5229264E-04 8.2168579E-03 at 160iterations 2.5203943E-04 5.4798126E-03 at 170iterations 1.8382024E-04 3.8185120E-03 at 180iterations finished qdiffx linear iterations at : 04:11:37 total time elapsed so far: 12.04000 # loops : 180 mean,max change (kT/e) : 1.8382024E-04 3.8185120E-03 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 04:11:37 12.181u 0.222s 0:12.73 97.4% 0+0k 0+0io 0pf+0w