Sun Feb 12 05:22:07 PST 2012 #!/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_thin.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 Feb 12 2012 at 05:22:08 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: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4883 !!! WARNING: HIZ 293 has a net charge of 0.2000 !!! WARNING: HIZ 297 has a net charge of 0.2000 !!! WARNING: GLM 316 has a net charge of -0.8000 !!! WARNING: ASP 608 has a net charge of -2.0000 !!! WARNING: ZN1 901 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5392305 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): -19.41100 46.60900 ymin,ymax (A): 8.106000 73.11600 zmin,zma (A): 33.70100 95.40100 x,y,z range (A): 66.02000 65.00999 61.70000 scale (grids/A): 0.5392305 object centre (A): 13.59900 40.61100 64.55100 number of atom coordinates read : 4883 total number of charged atoms : 4644 net assigned charge : -0.9999646 assigned positive charge : 726.2723 centred at (gu) : 90.22553 90.96852 89.71351 assigned negative charge : -727.2772 centred at (gu) : 90.21529 90.93708 89.74884 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8780 nv = 96 ne = 84 npr = 104409 no. pairs analyzed = 104409 no. exposed pairs = 5673 no. arc points = 38153 no. surface atoms = 1908 nbur = 2975 mkacc time = 0.2200000 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 = 1.596000 m= 326 mr = 4881 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3763 ## 454 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 11748 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6294128E-10 -3.2604938E-10 midg,1,midg; midg,igrid,midg -2.4887092E-10 2.7209737E-10 1,midg,midg; igrid,midg,midg -1.3058504E-10 3.6494620E-11 gauss-seidel spectral radius is 0.9824011 estimated iterations to convergence 62 setup time was (sec) 0.7000000 now iterating at: 05:22:09 rms-change max change #iterations 8.8115662E-02 11.46237 at 10iterations 6.1641899E-03 0.8995056 at 20iterations 8.0094958E-04 0.1289902 at 30iterations 2.9666093E-04 3.9642334E-02 at 40iterations 1.3360319E-04 1.7434120E-02 at 50iterations finished qdiffx linear iterations at : 05:22:14 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.3360319E-04 1.7434120E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 05:22:14 3.528u 0.192s 0:06.81 54.4% 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 Feb 12 2012 at 05:22:15 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: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4883 !!! WARNING: HIZ 293 has a net charge of 0.2000 !!! WARNING: HIZ 297 has a net charge of 0.2000 !!! WARNING: GLM 316 has a net charge of -0.8000 !!! WARNING: ASP 608 has a net charge of -2.0000 !!! WARNING: ZN1 901 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.617692 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): -19.41100 46.60900 ymin,ymax (A): 8.106000 73.11600 zmin,zma (A): 33.70100 95.40100 x,y,z range (A): 66.02000 65.00999 61.70000 scale (grids/A): 1.617692 object centre (A): 13.59900 40.61100 64.55100 number of atom coordinates read : 4883 total number of charged atoms : 4644 net assigned charge : -0.9999646 assigned positive charge : 726.2723 centred at (gu) : 90.67482 92.90411 89.13883 assigned negative charge : -727.2772 centred at (gu) : 90.64532 92.81075 89.24642 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 99462 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38153 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31111 mr = 71229 m= 3249 mr = 21784 m= 92 mr = 1594 m= 0 mr = 9 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 887 time to turn everything in is 0.6600000 number of dielectric boundary points 39298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 407 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 35502 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) : 0.5392305 object centre at (A) : 13.59900 40.61100 64.55100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6991880E-03 7.3627890E-03 midg,1,midg; midg,igrid,midg -6.4331628E-03 -9.9997176E-03 1,midg,midg; igrid,midg,midg -3.3764776E-02 1.1307665E-03 gauss-seidel spectral radius is 0.9983253 estimated iterations to convergence 194 setup time was (sec) 0.9500000 now iterating at: 05:22:16 rms-change max change #iterations 4.301168 163.7945 at 10iterations 1.860575 63.04471 at 20iterations 0.8031771 23.51282 at 30iterations 0.3468340 10.92312 at 40iterations 0.1501112 4.402954 at 50iterations 6.5105394E-02 2.067265 at 60iterations 2.8262381E-02 0.8674469 at 70iterations 1.2319169E-02 0.4095078 at 80iterations 5.4653338E-03 0.1804922 at 90iterations 2.5154797E-03 7.8022003E-02 at 100iterations 1.2564845E-03 4.0583372E-02 at 110iterations 7.2707166E-04 2.2933960E-02 at 120iterations finished qdiffx linear iterations at : 05:22:27 total time elapsed so far: 7.110000 # loops : 120 mean,max change (kT/e) : 7.2707166E-04 2.2933960E-02 energy calculations done at 7.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 05:22:29 7.288u 0.155s 0:14.06 52.8% 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 Feb 12 2012 at 05:22:29 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: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4883 !!! WARNING: HIZ 293 has a net charge of 0.2000 !!! WARNING: HIZ 297 has a net charge of 0.2000 !!! WARNING: GLM 316 has a net charge of -0.8000 !!! WARNING: ASP 608 has a net charge of -2.0000 !!! WARNING: ZN1 901 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.426537 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): -19.41100 46.60900 ymin,ymax (A): 8.106000 73.11600 zmin,zma (A): 33.70100 95.40100 x,y,z range (A): 66.02000 65.00999 61.70000 scale (grids/A): 2.426537 object centre (A): 13.59900 40.61100 64.55100 number of atom coordinates read : 4883 total number of charged atoms : 4644 net assigned charge : -0.9999646 assigned positive charge : 726.2723 centred at (gu) : 91.01172 94.35580 88.70792 assigned negative charge : -727.2772 centred at (gu) : 90.96791 94.21600 88.86935 start vw surface at 0.1700000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 231945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38153 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 108251 mr = 174232 m= 30975 mr = 86745 m= 4988 mr = 23432 m= 351 mr = 3218 m= 8 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 2984 time to turn everything in is 1.620000 number of dielectric boundary points 88726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 37112 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) : 1.617692 object centre at (A) : 13.59900 40.61100 64.55100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3263770E-02 0.1173974 midg,1,midg; midg,igrid,midg -0.1426539 -0.1406672 1,midg,midg; igrid,midg,midg -0.7310271 3.1809658E-02 gauss-seidel spectral radius is 0.9992166 estimated iterations to convergence 282 setup time was (sec) 1.910000 now iterating at: 05:22:32 rms-change max change #iterations 11.15907 280.8291 at 10iterations 6.503435 168.8676 at 20iterations 3.770596 82.75592 at 30iterations 2.176417 47.77332 at 40iterations 1.249015 22.59032 at 50iterations 0.7180946 12.93634 at 60iterations 0.4106979 7.190695 at 70iterations 0.2345097 4.538688 at 80iterations 0.1335067 2.261840 at 90iterations 7.6151803E-02 1.514081 at 100iterations 4.3369196E-02 0.9194443 at 110iterations 2.4691075E-02 0.4413905 at 120iterations 1.4072331E-02 0.2340012 at 130iterations 8.0730962E-03 0.1514587 at 140iterations 4.6660379E-03 7.8829288E-02 at 150iterations 2.7435059E-03 4.9360275E-02 at 160iterations 1.6710227E-03 3.0221939E-02 at 170iterations 1.0715920E-03 1.8104553E-02 at 180iterations finished qdiffx linear iterations at : 05:22:49 total time elapsed so far: 11.71000 # loops : 180 mean,max change (kT/e) : 1.0715920E-03 1.8104553E-02 energy calculations done at 11.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.88000 DelPhi exited at 05:22:49 11.881u 0.217s 0:20.79 58.1% 0+0k 0+0io 0pf+0w