Wed Dec 21 14:59:28 PST 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 Wed Dec 21 2011 at 14:59:28 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 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: 0.6420199 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): -27.27400 26.27500 ymin,ymax (A): 8.467000 52.48900 zmin,zma (A): -11.84900 43.60100 x,y,z range (A): 53.54900 44.02200 55.45000 scale (grids/A): 0.6420199 object centre (A): -0.4995003 30.47800 15.87600 number of atom coordinates read : 2339 total number of charged atoms : 2204 net assigned charge : 7.000027 assigned positive charge : 339.8564 centred at (gu) : 90.83644 90.84096 91.01761 assigned negative charge : -332.8571 centred at (gu) : 90.86831 90.72273 91.00208 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6761 nv = 96 ne = 84 npr = 46632 no. pairs analyzed = 46632 no. exposed pairs = 3210 no. arc points = 23309 no. surface atoms = 1065 nbur = 1274 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 360 mr = 3434 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.1800000 number of dielectric boundary points 3656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2216 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7830 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3535698E-09 1.5221572E-08 midg,1,midg; midg,igrid,midg -1.5393097E-09 2.7499135E-08 1,midg,midg; igrid,midg,midg 1.1790038E-08 8.6408161E-09 gauss-seidel spectral radius is 0.9874194 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 14:59:29 rms-change max change #iterations 0.1349036 20.92974 at 10iterations 1.3225321E-02 1.721000 at 20iterations 1.3073459E-03 0.1988907 at 30iterations 1.2947699E-04 2.1572113E-02 at 40iterations 1.3241204E-05 1.8997192E-03 at 50iterations finished qdiffx linear iterations at : 14:59:32 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.3241204E-05 1.8997192E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 14:59:32 3.482u 0.242s 0:04.09 90.9% 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 Dec 21 2011 at 14:59:32 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 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: 1.926060 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): -27.27400 26.27500 ymin,ymax (A): 8.467000 52.48900 zmin,zma (A): -11.84900 43.60100 x,y,z range (A): 53.54900 44.02200 55.45000 scale (grids/A): 1.926060 object centre (A): -0.4995003 30.47800 15.87600 number of atom coordinates read : 2339 total number of charged atoms : 2204 net assigned charge : 7.000027 assigned positive charge : 339.8564 centred at (gu) : 92.50925 92.52248 93.05257 assigned negative charge : -332.8571 centred at (gu) : 92.60512 92.16832 93.00641 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71363 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23309 grid for indexing accessible points = 1.400000 m= 25507 mr = 47045 m= 4011 mr = 17763 m= 248 mr = 2373 m= 5 mr = 93 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 248 time to turn everything in is 0.3500000 number of dielectric boundary points 33858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17384 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) : 0.6420199 object centre at (A) : -0.4995003 30.47800 15.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1692570E-02 1.7839033E-02 midg,1,midg; midg,igrid,midg -1.2235036E-02 1.8152148E-02 1,midg,midg; igrid,midg,midg 3.4626678E-02 3.6190324E-02 gauss-seidel spectral radius is 0.9986541 estimated iterations to convergence 216 setup time was (sec) 0.5700000 now iterating at: 14:59:33 rms-change max change #iterations 3.977896 193.8713 at 10iterations 1.871577 71.70150 at 20iterations 0.8820540 31.62216 at 30iterations 0.4129744 15.03884 at 40iterations 0.1939703 6.517094 at 50iterations 9.1048338E-02 3.120532 at 60iterations 4.2859334E-02 1.312693 at 70iterations 2.0134710E-02 0.6631508 at 80iterations 9.4720498E-03 0.2997432 at 90iterations 4.4626039E-03 0.1575623 at 100iterations 2.1005315E-03 7.1380615E-02 at 110iterations 9.8535977E-04 3.2775879E-02 at 120iterations finished qdiffx linear iterations at : 14:59:40 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 9.8535977E-04 3.2775879E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 14:59:41 7.932u 0.259s 0:08.70 94.0% 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 Dec 21 2011 at 14:59:41 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 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: 2.889089 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): -27.27400 26.27500 ymin,ymax (A): 8.467000 52.48900 zmin,zma (A): -11.84900 43.60100 x,y,z range (A): 53.54900 44.02200 55.45000 scale (grids/A): 2.889089 object centre (A): -0.4995003 30.47800 15.87600 number of atom coordinates read : 2339 total number of charged atoms : 2204 net assigned charge : 7.000027 assigned positive charge : 339.8564 centred at (gu) : 93.76368 93.78356 94.57877 assigned negative charge : -332.8571 centred at (gu) : 93.90762 93.25256 94.50961 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 164848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23309 grid for indexing accessible points = 1.400000 m= 81295 mr = 114604 m= 29563 mr = 64411 m= 7136 mr = 22866 m= 1046 mr = 5110 m= 71 mr = 710 m= 2 mr = 36 m= 0 mr = 2 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 792 time to turn everything in is 0.9100000 number of dielectric boundary points 76222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 17631 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) : 1.926060 object centre at (A) : -0.4995003 30.47800 15.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7104983 0.2101753 midg,1,midg; midg,igrid,midg -0.1239321 0.1298767 1,midg,midg; igrid,midg,midg 0.3604250 0.2794388 gauss-seidel spectral radius is 0.9992765 estimated iterations to convergence 293 setup time was (sec) 1.160000 now iterating at: 14:59:42 rms-change max change #iterations 9.563338 459.7302 at 10iterations 5.698430 165.1893 at 20iterations 3.354388 76.56702 at 30iterations 1.966954 49.06774 at 40iterations 1.151039 24.88567 at 50iterations 0.6722109 15.96882 at 60iterations 0.3905203 7.580950 at 70iterations 0.2269522 4.727571 at 80iterations 0.1318355 2.755699 at 90iterations 7.6441951E-02 1.731929 at 100iterations 4.4250894E-02 0.8392005 at 110iterations 2.5661968E-02 0.4951129 at 120iterations 1.4898949E-02 0.3274994 at 130iterations 8.6055640E-03 0.1752272 at 140iterations 4.9798205E-03 0.1073256 at 150iterations 2.8807162E-03 5.3682327E-02 at 160iterations 1.6675772E-03 3.2022476E-02 at 170iterations 9.6448796E-04 1.9378662E-02 at 180iterations finished qdiffx linear iterations at : 14:59:54 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 9.6448796E-04 1.9378662E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 14:59:55 13.056u 0.229s 0:13.70 96.8% 0+0k 0+0io 0pf+0w