Mon Oct 10 09:12:59 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 09:12:59 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 = 1962 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: 0.6421009 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): -6.088000 34.91300 ymin,ymax (A): -4.259000 49.53100 zmin,zma (A): -24.49600 30.94700 x,y,z range (A): 41.00100 53.79000 55.44300 scale (grids/A): 0.6421009 object centre (A): 14.41250 22.63600 3.225500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 90.89001 92.58646 90.24119 assigned negative charge : -282.8263 centred at (gu) : 90.95118 92.67604 90.19364 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5555 nv = 96 ne = 84 npr = 39960 no. pairs analyzed = 39960 no. exposed pairs = 2437 no. arc points = 17281 no. surface atoms = 830 nbur = 1132 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 306 mr = 3130 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.2600000 number of dielectric boundary points 2689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1720 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6555 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5196452E-09 1.2800919E-08 midg,1,midg; midg,igrid,midg 9.2483647E-09 -6.3549754E-10 1,midg,midg; igrid,midg,midg 1.1092268E-08 2.8875993E-09 gauss-seidel spectral radius is 0.9873772 estimated iterations to convergence 73 setup time was (sec) 0.5000000 now iterating at: 09:12:59 rms-change max change #iterations 0.1245042 20.35978 at 10iterations 1.2532402E-02 2.059834 at 20iterations 1.2428937E-03 0.2120590 at 30iterations 1.2169686E-04 1.9855261E-02 at 40iterations 1.2304028E-05 1.8005371E-03 at 50iterations finished qdiffx linear iterations at : 09:13:02 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.2304028E-05 1.8005371E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 09:13:02 3.341u 0.142s 0:03.75 92.8% 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 09:13:02 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 = 1962 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: 1.926303 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): -6.088000 34.91300 ymin,ymax (A): -4.259000 49.53100 zmin,zma (A): -24.49600 30.94700 x,y,z range (A): 41.00100 53.79000 55.44300 scale (grids/A): 1.926303 object centre (A): 14.41250 22.63600 3.225500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 92.67002 97.75929 90.72367 assigned negative charge : -282.8263 centred at (gu) : 92.85369 98.02824 90.58126 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 60000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17281 grid for indexing accessible points = 1.400000 m= 22703 mr = 41852 m= 3494 mr = 17433 m= 174 mr = 2294 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 814 time to turn everything in is 0.4900000 number of dielectric boundary points 24743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 14406 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) : 0.6421009 object centre at (A) : 14.41250 22.63600 3.225500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6457626E-02 2.3611421E-02 midg,1,midg; midg,igrid,midg 2.6006909E-02 5.0808624E-03 1,midg,midg; igrid,midg,midg 8.7087108E-03 5.7283504E-04 gauss-seidel spectral radius is 0.9985859 estimated iterations to convergence 211 setup time was (sec) 0.7700000 now iterating at: 09:13:03 rms-change max change #iterations 3.644364 170.4133 at 10iterations 1.690060 65.48711 at 20iterations 0.7793807 28.38678 at 30iterations 0.3614793 14.27878 at 40iterations 0.1667563 5.681214 at 50iterations 7.6916419E-02 2.549884 at 60iterations 3.5486709E-02 1.132851 at 70iterations 1.6374946E-02 0.6395407 at 80iterations 7.5748391E-03 0.2936859 at 90iterations 3.4912773E-03 0.1147594 at 100iterations 1.6210291E-03 5.7521820E-02 at 110iterations 7.4967090E-04 3.1602383E-02 at 120iterations finished qdiffx linear iterations at : 09:13:10 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 7.4967090E-04 3.1602383E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 09:13:11 7.753u 0.242s 0:08.27 96.6% 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 09:13:11 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 = 1962 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: 2.889454 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): -6.088000 34.91300 ymin,ymax (A): -4.259000 49.53100 zmin,zma (A): -24.49600 30.94700 x,y,z range (A): 41.00100 53.79000 55.44300 scale (grids/A): 2.889454 object centre (A): 14.41250 22.63600 3.225500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 94.00513 101.6389 91.08553 assigned negative charge : -282.8263 centred at (gu) : 94.28062 102.0425 90.87193 start vw surface at 0.1300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 138553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17281 grid for indexing accessible points = 1.400000 m= 72459 mr = 100835 m= 27320 mr = 60705 m= 6211 mr = 22769 m= 702 mr = 4752 m= 38 mr = 464 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 2698 time to turn everything in is 1.180000 number of dielectric boundary points 55744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 14639 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) : 1.926303 object centre at (A) : 14.41250 22.63600 3.225500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.035372 0.1063401 midg,1,midg; midg,igrid,midg 0.2319929 3.5821027E-03 1,midg,midg; igrid,midg,midg 5.5677243E-02 7.9448642E-03 gauss-seidel spectral radius is 0.9992315 estimated iterations to convergence 285 setup time was (sec) 1.480000 now iterating at: 09:13:12 rms-change max change #iterations 8.601065 420.5819 at 10iterations 4.989470 123.1192 at 20iterations 2.854826 62.05626 at 30iterations 1.628803 41.65569 at 40iterations 0.9312704 19.09443 at 50iterations 0.5306668 10.89248 at 60iterations 0.3016386 6.604700 at 70iterations 0.1713971 3.243889 at 80iterations 9.7711064E-02 1.983040 at 90iterations 5.5524163E-02 1.044667 at 100iterations 3.1494528E-02 0.6448364 at 110iterations 1.7873516E-02 0.3897238 at 120iterations 1.0170493E-02 0.2072983 at 130iterations 5.7610450E-03 0.1083785 at 140iterations 3.2682368E-03 7.4449539E-02 at 150iterations 1.8578138E-03 3.5276413E-02 at 160iterations 1.0533218E-03 2.0798683E-02 at 170iterations 5.9969141E-04 1.2394428E-02 at 180iterations finished qdiffx linear iterations at : 09:13:23 total time elapsed so far: 12.38000 # loops : 180 mean,max change (kT/e) : 5.9969141E-04 1.2394428E-02 energy calculations done at 12.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 09:13:24 12.574u 0.239s 0:13.10 97.7% 0+0k 0+0io 0pf+0w