Sun Oct 9 12:09:50 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+sph2.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 = amb2.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 12:09:50 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2396 !!! WARNING: HIR 57 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6853403 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): -6.661000 42.97100 ymin,ymax (A): -13.73800 38.20700 zmin,zma (A): 0.8500000 45.10000 x,y,z range (A): 49.63200 51.94500 44.25000 scale (grids/A): 0.6853403 object centre (A): 18.15500 12.23450 22.97500 number of atom coordinates read : 2396 total number of charged atoms : 2254 net assigned charge : 3.514024 assigned positive charge : 370.9901 centred at (gu) : 90.22099 90.96152 91.09325 assigned negative charge : -367.4765 centred at (gu) : 90.25069 91.09326 91.18771 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7573 nv = 96 ne = 84 npr = 48627 no. pairs analyzed = 48627 no. exposed pairs = 2992 no. arc points = 21058 no. surface atoms = 1016 nbur = 1380 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 485 mr = 4203 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2028 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8659 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0920959E-08 -1.9184764E-08 midg,1,midg; midg,igrid,midg 5.2459928E-08 -3.4888519E-08 1,midg,midg; igrid,midg,midg 2.7365290E-08 8.1533971E-09 gauss-seidel spectral radius is 0.9889410 estimated iterations to convergence 78 setup time was (sec) 0.4800000 now iterating at: 12:09:51 rms-change max change #iterations 0.1906490 24.95913 at 10iterations 2.2610255E-02 2.842716 at 20iterations 2.9437374E-03 0.4307785 at 30iterations 5.1267247E-04 6.8565369E-02 at 40iterations 1.2467515E-04 1.5911102E-02 at 50iterations finished qdiffx linear iterations at : 12:09:53 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 1.2467515E-04 1.5911102E-02 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 12:09:54 3.057u 0.153s 0:03.47 92.2% 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 12:09:54 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2396 !!! WARNING: HIR 57 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.056021 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): -6.661000 42.97100 ymin,ymax (A): -13.73800 38.20700 zmin,zma (A): 0.8500000 45.10000 x,y,z range (A): 49.63200 51.94500 44.25000 scale (grids/A): 2.056021 object centre (A): 18.15500 12.23450 22.97500 number of atom coordinates read : 2396 total number of charged atoms : 2254 net assigned charge : 3.514024 assigned positive charge : 370.9901 centred at (gu) : 90.66255 92.88409 93.27934 assigned negative charge : -367.4765 centred at (gu) : 90.75184 93.27938 93.56284 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 79968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21058 grid for indexing accessible points = 1.400000 m= 31583 mr = 55410 m= 5865 mr = 23751 m= 497 mr = 3745 m= 11 mr = 227 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 326 time to turn everything in is 0.5600000 number of dielectric boundary points 34791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17888 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) : 0.6853403 object centre at (A) : 18.15500 12.23450 22.97500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3472946E-02 3.9663706E-03 midg,1,midg; midg,igrid,midg 2.0866923E-02 -4.0241469E-02 1,midg,midg; igrid,midg,midg 3.9870579E-02 -2.4196628E-02 gauss-seidel spectral radius is 0.9988008 estimated iterations to convergence 229 setup time was (sec) 0.8300000 now iterating at: 12:09:55 rms-change max change #iterations 4.834458 234.2537 at 10iterations 2.363156 75.40015 at 20iterations 1.158041 35.89433 at 30iterations 0.5681619 16.90414 at 40iterations 0.2802097 9.670021 at 50iterations 0.1378973 4.353622 at 60iterations 6.7999147E-02 1.897901 at 70iterations 3.3457253E-02 1.022663 at 80iterations 1.6533611E-02 0.5182610 at 90iterations 8.1852674E-03 0.2389374 at 100iterations 4.0867832E-03 0.1258850 at 110iterations 2.0616504E-03 5.6274414E-02 at 120iterations finished qdiffx linear iterations at : 12:10:01 total time elapsed so far: 6.870000 # loops : 120 mean,max change (kT/e) : 2.0616504E-03 5.6274414E-02 energy calculations done at 6.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 12:10:01 7.050u 0.165s 0:07.52 95.8% 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 12:10:01 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2396 !!! WARNING: HIR 57 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 3.084031 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): -6.661000 42.97100 ymin,ymax (A): -13.73800 38.20700 zmin,zma (A): 0.8500000 45.10000 x,y,z range (A): 49.63200 51.94500 44.25000 scale (grids/A): 3.084031 object centre (A): 18.15500 12.23450 22.97500 number of atom coordinates read : 2396 total number of charged atoms : 2254 net assigned charge : 3.514024 assigned positive charge : 370.9901 centred at (gu) : 90.99377 94.32596 94.91889 assigned negative charge : -367.4765 centred at (gu) : 91.12771 94.91908 95.34422 start vw surface at 0.2100000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 184520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21058 grid for indexing accessible points = 1.400000 m= 98271 mr = 133837 m= 39749 mr = 81090 m= 11127 mr = 32622 m= 2022 mr = 8414 m= 214 mr = 1370 m= 4 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 1061 time to turn everything in is 1.850000 number of dielectric boundary points 78457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 18032 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) : 2.056021 object centre at (A) : 18.15500 12.23450 22.97500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3709729 -8.0746196E-02 midg,1,midg; midg,igrid,midg 0.4342616 -0.3512208 1,midg,midg; igrid,midg,midg 0.4425468 -0.5504069 gauss-seidel spectral radius is 0.9992915 estimated iterations to convergence 296 setup time was (sec) 2.130000 now iterating at: 12:10:04 rms-change max change #iterations 10.98522 428.7979 at 10iterations 6.542543 140.7681 at 20iterations 3.865323 70.14919 at 30iterations 2.280628 43.43580 at 40iterations 1.346259 27.40125 at 50iterations 0.7908260 14.91902 at 60iterations 0.4643644 7.858597 at 70iterations 0.2725423 4.711508 at 80iterations 0.1598844 2.891317 at 90iterations 9.3449324E-02 1.674979 at 100iterations 5.4696213E-02 1.062510 at 110iterations 3.2224759E-02 0.5335331 at 120iterations 1.8968562E-02 0.3446617 at 130iterations 1.1258245E-02 0.2189713 at 140iterations 6.7952732E-03 0.1305084 at 150iterations 4.1906429E-03 8.5990906E-02 at 160iterations 2.6786798E-03 5.7098389E-02 at 170iterations 1.7912713E-03 3.9306641E-02 at 180iterations finished qdiffx linear iterations at : 12:10:13 total time elapsed so far: 11.55000 # loops : 180 mean,max change (kT/e) : 1.7912713E-03 3.9306641E-02 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.73000 DelPhi exited at 12:10:14 11.735u 0.176s 0:12.20 97.5% 0+0k 0+0io 0pf+0w