Sun Oct 9 22:30:47 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 22:30:47 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3020 !!! WARNING: HIZ 21 has a net charge of 0.2000 !!! WARNING: GLM 40 has a net charge of -0.6000 !!! WARNING: ZN1 1035 has a net charge of 1.4000 !!! WARNING: ZN1 1036 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5774440 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): -28.43000 29.28200 ymin,ymax (A): 41.10000 102.7510 zmin,zma (A): 52.20500 109.7260 x,y,z range (A): 57.71200 61.65100 57.52100 scale (grids/A): 0.5774440 object centre (A): 0.4259996 71.92550 80.96550 number of atom coordinates read : 3020 total number of charged atoms : 2907 net assigned charge : 8.900018 assigned positive charge : 465.2859 centred at (gu) : 89.64081 88.85947 90.49480 assigned negative charge : -456.3872 centred at (gu) : 89.64166 88.74024 90.47359 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6734 nv = 96 ne = 84 npr = 56463 no. pairs analyzed = 56463 no. exposed pairs = 4239 no. arc points = 31492 no. surface atoms = 1409 nbur = 1611 mkacc time = 0.1200000 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 = 1.484000 m= 301 mr = 3131 m= 2 mr = 9 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 0.3000000 number of dielectric boundary points 3897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3152 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8621 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2230742E-09 2.5168359E-09 midg,1,midg; midg,igrid,midg -9.5362573E-10 3.2535301E-09 1,midg,midg; igrid,midg,midg 1.9804740E-09 1.6488301E-09 gauss-seidel spectral radius is 0.9845423 estimated iterations to convergence 66 setup time was (sec) 0.5100000 now iterating at: 22:30:48 rms-change max change #iterations 9.6334204E-02 16.63718 at 10iterations 7.3194019E-03 1.214470 at 20iterations 5.6052249E-04 8.3145142E-02 at 30iterations 4.3981843E-05 6.3629150E-03 at 40iterations 3.5193750E-06 5.0544739E-04 at 50iterations finished qdiffx linear iterations at : 22:30:51 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 3.5193750E-06 5.0544739E-04 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 22:30:51 3.285u 0.249s 0:03.98 88.4% 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 Sun Oct 9 2011 at 22:30:52 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3020 !!! WARNING: HIZ 21 has a net charge of 0.2000 !!! WARNING: GLM 40 has a net charge of -0.6000 !!! WARNING: ZN1 1035 has a net charge of 1.4000 !!! WARNING: ZN1 1036 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.732332 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): -28.43000 29.28200 ymin,ymax (A): 41.10000 102.7510 zmin,zma (A): 52.20500 109.7260 x,y,z range (A): 57.71200 61.65100 57.52100 scale (grids/A): 1.732332 object centre (A): 0.4259996 71.92550 80.96550 number of atom coordinates read : 3020 total number of charged atoms : 2907 net assigned charge : 8.900018 assigned positive charge : 465.2859 centred at (gu) : 88.92150 86.57765 91.48389 assigned negative charge : -456.3872 centred at (gu) : 88.92467 86.22047 91.42048 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31492 grid for indexing accessible points = 1.400000 m= 22780 mr = 46177 m= 2629 mr = 15039 m= 106 mr = 1297 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 239 time to turn everything in is 0.5300000 number of dielectric boundary points 36317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 308 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 22554 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) : 0.5774440 object centre at (A) : 0.4259996 71.92550 80.96550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8820640E-03 2.4855589E-02 midg,1,midg; midg,igrid,midg -3.4238591E-03 1.2798009E-02 1,midg,midg; igrid,midg,midg 1.5984381E-02 1.7969394E-02 gauss-seidel spectral radius is 0.9984279 estimated iterations to convergence 200 setup time was (sec) 0.8400000 now iterating at: 22:30:53 rms-change max change #iterations 3.826815 178.9359 at 10iterations 1.673705 60.62151 at 20iterations 0.7388548 26.29366 at 30iterations 0.3259773 11.12910 at 40iterations 0.1433869 5.192369 at 50iterations 6.3482374E-02 2.447807 at 60iterations 2.7997095E-02 1.071287 at 70iterations 1.2379672E-02 0.4489441 at 80iterations 5.4723090E-03 0.1848354 at 90iterations 2.4265929E-03 7.7106237E-02 at 100iterations 1.0720819E-03 3.5053253E-02 at 110iterations 4.7428408E-04 1.5133381E-02 at 120iterations finished qdiffx linear iterations at : 22:30:59 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 4.7428408E-04 1.5133381E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 22:31:00 7.557u 0.246s 0:08.16 95.4% 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 Sun Oct 9 2011 at 22:31:00 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3020 !!! WARNING: HIZ 21 has a net charge of 0.2000 !!! WARNING: GLM 40 has a net charge of -0.6000 !!! WARNING: ZN1 1035 has a net charge of 1.4000 !!! WARNING: ZN1 1036 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: 2.598498 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): -28.43000 29.28200 ymin,ymax (A): 41.10000 102.7510 zmin,zma (A): 52.20500 109.7260 x,y,z range (A): 57.71200 61.65100 57.52100 scale (grids/A): 2.598498 object centre (A): 0.4259996 71.92550 80.96550 number of atom coordinates read : 3020 total number of charged atoms : 2907 net assigned charge : 8.900018 assigned positive charge : 465.2859 centred at (gu) : 88.38188 84.86625 92.22536 assigned negative charge : -456.3872 centred at (gu) : 88.38696 84.33056 92.13064 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 169735 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31492 grid for indexing accessible points = 1.400000 m= 76803 mr = 113619 m= 23063 mr = 58956 m= 4161 mr = 16811 m= 438 mr = 2670 m= 6 mr = 227 m= 0 mr = 1 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 875 time to turn everything in is 1.260000 number of dielectric boundary points 81922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 23240 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) : 1.732332 object centre at (A) : 0.4259996 71.92550 80.96550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2177163 0.1098964 midg,1,midg; midg,igrid,midg -0.1791959 0.2714736 1,midg,midg; igrid,midg,midg 0.3246198 0.1400108 gauss-seidel spectral radius is 0.9992281 estimated iterations to convergence 284 setup time was (sec) 1.570000 now iterating at: 22:31:02 rms-change max change #iterations 9.703021 345.3782 at 10iterations 5.687332 148.5957 at 20iterations 3.314117 81.67621 at 30iterations 1.912221 51.40985 at 40iterations 1.103712 24.38644 at 50iterations 0.6336061 13.64990 at 60iterations 0.3634472 8.406038 at 70iterations 0.2083609 4.841753 at 80iterations 0.1190639 2.315581 at 90iterations 6.7784838E-02 1.327217 at 100iterations 3.8674846E-02 0.8113441 at 110iterations 2.2072036E-02 0.4781113 at 120iterations 1.2558191E-02 0.2935686 at 130iterations 7.1587097E-03 0.1427021 at 140iterations 4.0693027E-03 8.6063385E-02 at 150iterations 2.3131904E-03 4.7588348E-02 at 160iterations 1.3151582E-03 2.3468971E-02 at 170iterations 7.4725103E-04 1.5583992E-02 at 180iterations finished qdiffx linear iterations at : 22:31:12 total time elapsed so far: 12.03000 # loops : 180 mean,max change (kT/e) : 7.4725103E-04 1.5583992E-02 energy calculations done at 12.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 22:31:13 12.217u 0.263s 0:12.79 97.4% 0+0k 0+0io 0pf+0w