Mon Oct 10 17:03:34 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 Mon Oct 10 2011 at 17:03:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3180 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: 0.5914112 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): -8.967000 48.87800 ymin,ymax (A): -7.925000 43.85100 zmin,zma (A): -4.698000 55.49700 x,y,z range (A): 57.84500 51.77600 60.19500 scale (grids/A): 0.5914112 object centre (A): 19.95550 17.96300 25.39950 number of atom coordinates read : 3180 total number of charged atoms : 3038 net assigned charge : -2.999963 assigned positive charge : 477.6535 centred at (gu) : 89.73479 88.44650 89.14857 assigned negative charge : -480.6548 centred at (gu) : 89.69722 88.35992 89.03667 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7336 nv = 96 ne = 84 npr = 64165 no. pairs analyzed = 64165 no. exposed pairs = 4065 no. arc points = 28515 no. surface atoms = 1379 nbur = 1801 mkacc time = 0.1400000 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 = 1.456000 m= 290 mr = 3863 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2899 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9293 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8111849E-09 2.3926645E-09 midg,1,midg; midg,igrid,midg -5.5694063E-09 1.4363818E-09 1,midg,midg; igrid,midg,midg -2.3009972E-09 3.8934048E-10 gauss-seidel spectral radius is 0.9852579 estimated iterations to convergence 68 setup time was (sec) 0.5700000 now iterating at: 17:03:35 rms-change max change #iterations 0.1140461 18.54798 at 10iterations 9.3265073E-03 1.569832 at 20iterations 7.5514306E-04 0.1087570 at 30iterations 6.3436288E-05 1.0815620E-02 at 40iterations 5.3252420E-06 7.2097778E-04 at 50iterations finished qdiffx linear iterations at : 17:03:37 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 5.3252420E-06 7.2097778E-04 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 17:03:40 3.217u 0.154s 0:05.52 60.8% 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 Mon Oct 10 2011 at 17:03:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3180 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: 1.774234 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): -8.967000 48.87800 ymin,ymax (A): -7.925000 43.85100 zmin,zma (A): -4.698000 55.49700 x,y,z range (A): 57.84500 51.77600 60.19500 scale (grids/A): 1.774234 object centre (A): 19.95550 17.96300 25.39950 number of atom coordinates read : 3180 total number of charged atoms : 3038 net assigned charge : -2.999963 assigned positive charge : 477.6535 centred at (gu) : 89.20321 85.33862 87.44468 assigned negative charge : -480.6548 centred at (gu) : 89.09132 85.07909 87.10972 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 79980 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28515 grid for indexing accessible points = 1.400000 m= 25675 mr = 54361 m= 3050 mr = 17974 m= 127 mr = 1612 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1019 time to turn everything in is 0.5200000 number of dielectric boundary points 34866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 302 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 23654 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) : 0.5914112 object centre at (A) : 19.95550 17.96300 25.39950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2717648E-02 -3.3454837E-03 midg,1,midg; midg,igrid,midg -2.7287332E-02 2.2323297E-03 1,midg,midg; igrid,midg,midg -3.6399789E-02 1.2640173E-02 gauss-seidel spectral radius is 0.9984865 estimated iterations to convergence 204 setup time was (sec) 0.8000000 now iterating at: 17:03:41 rms-change max change #iterations 4.136537 165.4895 at 10iterations 1.846442 62.11853 at 20iterations 0.8287390 28.52290 at 30iterations 0.3733531 12.25867 at 40iterations 0.1679165 5.381594 at 50iterations 7.5347416E-02 2.443100 at 60iterations 3.3773489E-02 1.059825 at 70iterations 1.5217208E-02 0.4983465 at 80iterations 6.8305484E-03 0.2174816 at 90iterations 3.0789629E-03 0.1066265 at 100iterations 1.3852610E-03 4.2784214E-02 at 110iterations 6.2473683E-04 2.0371675E-02 at 120iterations finished qdiffx linear iterations at : 17:03:47 total time elapsed so far: 7.090000 # loops : 120 mean,max change (kT/e) : 6.2473683E-04 2.0371675E-02 energy calculations done at 7.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.270000 DelPhi exited at 17:03:48 7.269u 0.195s 0:07.78 95.7% 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 Mon Oct 10 2011 at 17:03:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3180 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: 2.661351 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): -8.967000 48.87800 ymin,ymax (A): -7.925000 43.85100 zmin,zma (A): -4.698000 55.49700 x,y,z range (A): 57.84500 51.77600 60.19500 scale (grids/A): 2.661351 object centre (A): 19.95550 17.96300 25.39950 number of atom coordinates read : 3180 total number of charged atoms : 3038 net assigned charge : -2.999963 assigned positive charge : 477.6535 centred at (gu) : 88.80469 83.00767 86.16676 assigned negative charge : -480.6548 centred at (gu) : 88.63686 82.61869 85.66453 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 185404 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28515 grid for indexing accessible points = 1.400000 m= 86884 mr = 132544 m= 26773 mr = 69301 m= 4969 mr = 20507 m= 549 mr = 3367 m= 24 mr = 291 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 3424 time to turn everything in is 1.300000 number of dielectric boundary points 78593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 24297 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) : 1.774234 object centre at (A) : 19.95550 17.96300 25.39950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2440192 -0.3342761 midg,1,midg; midg,igrid,midg -0.3143007 2.6101828E-02 1,midg,midg; igrid,midg,midg -0.4569083 0.2357612 gauss-seidel spectral radius is 0.9992375 estimated iterations to convergence 286 setup time was (sec) 1.590000 now iterating at: 17:03:49 rms-change max change #iterations 10.16350 411.8267 at 10iterations 5.937463 150.6474 at 20iterations 3.422351 76.72023 at 30iterations 1.966802 46.70689 at 40iterations 1.131278 20.52398 at 50iterations 0.6484972 13.74075 at 60iterations 0.3704083 7.079387 at 70iterations 0.2113397 3.823794 at 80iterations 0.1206342 2.278141 at 90iterations 6.8728320E-02 1.213491 at 100iterations 3.9173115E-02 0.7067661 at 110iterations 2.2288155E-02 0.4155474 at 120iterations 1.2686387E-02 0.2234471 at 130iterations 7.2232154E-03 0.1200943 at 140iterations 4.1103498E-03 7.6793671E-02 at 150iterations 2.3431438E-03 4.2083740E-02 at 160iterations 1.3304474E-03 2.4546504E-02 at 170iterations 7.5841701E-04 1.4221191E-02 at 180iterations finished qdiffx linear iterations at : 17:03:59 total time elapsed so far: 11.37000 # loops : 180 mean,max change (kT/e) : 7.5841701E-04 1.4221191E-02 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.57000 DelPhi exited at 17:04:01 11.574u 0.213s 0:13.21 89.1% 0+0k 0+0io 0pf+0w