Sat Oct 15 13:25:30 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 Sat Oct 15 2011 at 13:25:31 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 = 1044 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7306911 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): -28.66400 10.73000 ymin,ymax (A): 1.353000 42.64100 zmin,zma (A): 11.08300 59.80400 x,y,z range (A): 39.39400 41.28800 48.72100 scale (grids/A): 0.7306911 object centre (A): -8.966999 21.99700 35.44350 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 145.2251 centred at (gu) : 91.93069 91.56055 91.53934 assigned negative charge : -143.7250 centred at (gu) : 91.74604 91.69187 91.23804 start vw surface at 5.9999999E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4062 nv = 96 ne = 84 npr = 20221 no. pairs analyzed = 20221 no. exposed pairs = 1635 no. arc points = 12155 no. surface atoms = 551 nbur = 493 mkacc time = 4.0000003E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 310 mr = 1824 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 5.0000001E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1100000 number of dielectric boundary points 2492 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 961 ## 80 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 3943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1687154E-08 1.7304636E-07 midg,1,midg; midg,igrid,midg 5.0333767E-08 -4.2109285E-08 1,midg,midg; igrid,midg,midg -3.4958127E-08 1.2616275E-07 gauss-seidel spectral radius is 0.9901441 estimated iterations to convergence 82 setup time was (sec) 0.3400000 now iterating at: 13:25:31 rms-change max change #iterations 0.1521063 27.21155 at 10iterations 1.9751303E-02 4.599524 at 20iterations 2.5009562E-03 0.4306707 at 30iterations 3.2402462E-04 5.7967186E-02 at 40iterations 4.1436899E-05 7.9956055E-03 at 50iterations finished qdiffx linear iterations at : 13:25:34 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 4.1436899E-05 7.9956055E-03 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 13:25:35 3.784u 0.243s 0:04.32 93.0% 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 Sat Oct 15 2011 at 13:25:35 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 = 1044 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.192073 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): -28.66400 10.73000 ymin,ymax (A): 1.353000 42.64100 zmin,zma (A): 11.08300 59.80400 x,y,z range (A): 39.39400 41.28800 48.72100 scale (grids/A): 2.192073 object centre (A): -8.966999 21.99700 35.44350 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 145.2251 centred at (gu) : 95.79214 94.68167 94.61808 assigned negative charge : -143.7250 centred at (gu) : 95.23821 95.07578 93.71411 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 40845 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12155 grid for indexing accessible points = 1.400000 m= 15691 mr = 24138 m= 3787 mr = 11083 m= 450 mr = 2521 m= 16 mr = 208 m= 0 mr = 3 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 22836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 7311 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) : 0.7306911 object centre at (A) : -8.966999 21.99700 35.44350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1882756E-04 4.3988440E-02 midg,1,midg; midg,igrid,midg 2.1156592E-02 7.2078658E-03 1,midg,midg; igrid,midg,midg -8.5010882E-03 3.1250592E-03 gauss-seidel spectral radius is 0.9988090 estimated iterations to convergence 229 setup time was (sec) 0.5100000 now iterating at: 13:25:36 rms-change max change #iterations 3.237394 166.2529 at 10iterations 1.573554 84.34325 at 20iterations 0.7694411 38.08902 at 30iterations 0.3758207 15.85300 at 40iterations 0.1844161 7.349693 at 50iterations 9.0234652E-02 3.517700 at 60iterations 4.4114836E-02 1.959694 at 70iterations 2.1554427E-02 0.8930241 at 80iterations 1.0574254E-02 0.4172921 at 90iterations 5.1586851E-03 0.2210579 at 100iterations 2.5366868E-03 9.3980789E-02 at 110iterations 1.2425252E-03 5.0646007E-02 at 120iterations finished qdiffx linear iterations at : 13:25:44 total time elapsed so far: 8.570000 # loops : 120 mean,max change (kT/e) : 1.2425252E-03 5.0646007E-02 energy calculations done at 8.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.700000 DelPhi exited at 13:25:44 8.705u 0.272s 0:09.25 96.9% 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 Sat Oct 15 2011 at 13:25:44 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 = 1044 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.9999998E-03 grid size : 179 scale,in grids/A, set to be: 3.288110 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): -28.66400 10.73000 ymin,ymax (A): 1.353000 42.64100 zmin,zma (A): 11.08300 59.80400 x,y,z range (A): 39.39400 41.28800 48.72100 scale (grids/A): 3.288110 object centre (A): -8.966999 21.99700 35.44350 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 145.2251 centred at (gu) : 98.68825 97.02252 96.92706 assigned negative charge : -143.7250 centred at (gu) : 97.85734 97.61360 95.57121 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 93409 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12155 grid for indexing accessible points = 1.400000 m= 46278 mr = 58758 m= 21313 mr = 36060 m= 7383 mr = 17135 m= 1689 mr = 5687 m= 193 mr = 1135 m= 10 mr = 86 m= 0 mr = 5 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 51409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 7344 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) : 2.192073 object centre at (A) : -8.966999 21.99700 35.44350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7476281E-02 0.3075944 midg,1,midg; midg,igrid,midg 0.1593123 6.2987916E-02 1,midg,midg; igrid,midg,midg -3.0240079E-02 -1.0431343E-02 gauss-seidel spectral radius is 0.9992942 estimated iterations to convergence 297 setup time was (sec) 0.9800000 now iterating at: 13:25:45 rms-change max change #iterations 7.287616 316.7308 at 10iterations 4.317129 167.9958 at 20iterations 2.545767 70.94780 at 30iterations 1.496825 40.73453 at 40iterations 0.8764557 25.18618 at 50iterations 0.5111332 12.52501 at 60iterations 0.2976505 7.433905 at 70iterations 0.1734194 4.218571 at 80iterations 0.1009324 2.567022 at 90iterations 5.8571957E-02 1.549288 at 100iterations 3.4118745E-02 0.8293228 at 110iterations 1.9802209E-02 0.4313030 at 120iterations 1.1508078E-02 0.2833996 at 130iterations 6.6853906E-03 0.1706076 at 140iterations 3.8712951E-03 8.3074093E-02 at 150iterations 2.2546253E-03 4.9818829E-02 at 160iterations 1.3027604E-03 3.0451298E-02 at 170iterations 7.5552322E-04 1.6845703E-02 at 180iterations finished qdiffx linear iterations at : 13:25:58 total time elapsed so far: 13.71000 # loops : 180 mean,max change (kT/e) : 7.5552322E-04 1.6845703E-02 energy calculations done at 13.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.84000 DelPhi exited at 13:25:59 13.845u 0.289s 0:14.42 97.9% 0+0k 0+0io 0pf+0w