Mon Oct 10 18:47:55 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 18:47:55 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 = 2409 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: 0.5964448 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): -11.39400 48.29300 ymin,ymax (A): 61.66500 115.6370 zmin,zma (A): 45.08800 87.98900 x,y,z range (A): 59.68700 53.97200 42.90100 scale (grids/A): 0.5964448 object centre (A): 18.44950 88.65100 66.53850 number of atom coordinates read : 2409 total number of charged atoms : 2270 net assigned charge : -0.9999925 assigned positive charge : 361.8248 centred at (gu) : 87.77821 90.94730 90.92345 assigned negative charge : -362.8255 centred at (gu) : 87.82917 90.99494 91.04286 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5753 nv = 96 ne = 84 npr = 48397 no. pairs analyzed = 48397 no. exposed pairs = 3032 no. arc points = 21075 no. surface atoms = 1015 nbur = 1394 mkacc time = 9.9999994E-02 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= 273 mr = 3123 m= 0 mr = 26 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2877 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2106 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7142 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5874247E-09 -4.9958526E-09 midg,1,midg; midg,igrid,midg 8.5972252E-10 -2.2567044E-09 1,midg,midg; igrid,midg,midg 1.9981194E-09 -1.1556519E-09 gauss-seidel spectral radius is 0.9854377 estimated iterations to convergence 68 setup time was (sec) 0.5100000 now iterating at: 18:47:55 rms-change max change #iterations 0.1014666 15.74597 at 10iterations 8.6435322E-03 1.449833 at 20iterations 8.1011152E-04 0.1351433 at 30iterations 1.2627704E-04 2.4585724E-02 at 40iterations 2.9553265E-05 6.3991547E-03 at 50iterations finished qdiffx linear iterations at : 18:47:58 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 2.9553265E-05 6.3991547E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 18:47:58 3.152u 0.157s 0:03.70 89.1% 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 18:47:58 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 = 2409 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: 1.789334 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): -11.39400 48.29300 ymin,ymax (A): 61.66500 115.6370 zmin,zma (A): 45.08800 87.98900 x,y,z range (A): 59.68700 53.97200 42.90100 scale (grids/A): 1.789334 object centre (A): 18.44950 88.65100 66.53850 number of atom coordinates read : 2409 total number of charged atoms : 2270 net assigned charge : -0.9999925 assigned positive charge : 361.8248 centred at (gu) : 83.33397 92.84138 92.76957 assigned negative charge : -362.8255 centred at (gu) : 83.48731 92.98462 93.12842 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 62758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21075 grid for indexing accessible points = 1.400000 m= 21848 mr = 43658 m= 2890 mr = 15847 m= 109 mr = 1672 m= 0 mr = 23 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1224 time to turn everything in is 0.4300000 number of dielectric boundary points 26405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 17725 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) : 0.5964448 object centre at (A) : 18.44950 88.65100 66.53850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7373298E-03 -7.1470505E-03 midg,1,midg; midg,igrid,midg 1.6228225E-02 -1.1968610E-02 1,midg,midg; igrid,midg,midg -1.2082542E-02 -1.5152453E-02 gauss-seidel spectral radius is 0.9984340 estimated iterations to convergence 200 setup time was (sec) 0.7000000 now iterating at: 18:47:59 rms-change max change #iterations 3.605341 163.1253 at 10iterations 1.585475 65.31438 at 20iterations 0.7058645 25.95304 at 30iterations 0.3124723 11.97840 at 40iterations 0.1391109 4.757021 at 50iterations 6.1663087E-02 2.126589 at 60iterations 2.7355932E-02 0.9830418 at 70iterations 1.2212913E-02 0.4532089 at 80iterations 5.4379771E-03 0.2227783 at 90iterations 2.4540687E-03 9.0121269E-02 at 100iterations 1.1135380E-03 4.0318489E-02 at 110iterations 5.2127009E-04 1.8520355E-02 at 120iterations finished qdiffx linear iterations at : 18:48:06 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 5.2127009E-04 1.8520355E-02 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 18:48:06 7.103u 0.180s 0:07.58 96.0% 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 Mon Oct 10 2011 at 18:48:06 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 = 2409 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: 2.684001 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): -11.39400 48.29300 ymin,ymax (A): 61.66500 115.6370 zmin,zma (A): 45.08800 87.98900 x,y,z range (A): 59.68700 53.97200 42.90100 scale (grids/A): 2.684001 object centre (A): 18.44950 88.65100 66.53850 number of atom coordinates read : 2409 total number of charged atoms : 2270 net assigned charge : -0.9999925 assigned positive charge : 361.8248 centred at (gu) : 80.00075 94.26189 94.15436 assigned negative charge : -362.8255 centred at (gu) : 80.23086 94.47678 94.69261 start vw surface at 0.1500000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 145539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21075 grid for indexing accessible points = 1.400000 m= 71688 mr = 106118 m= 24691 mr = 58204 m= 4978 mr = 19555 m= 469 mr = 3559 m= 14 mr = 255 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 4105 time to turn everything in is 1.140000 number of dielectric boundary points 59688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 18154 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) : 1.789334 object centre at (A) : 18.44950 88.65100 66.53850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1892681E-02 -6.7752846E-02 midg,1,midg; midg,igrid,midg 0.2692406 -0.1853463 1,midg,midg; igrid,midg,midg -0.1863000 -3.8956299E-03 gauss-seidel spectral radius is 0.9991969 estimated iterations to convergence 279 setup time was (sec) 1.430000 now iterating at: 18:48:08 rms-change max change #iterations 8.801840 269.0329 at 10iterations 5.075727 125.6513 at 20iterations 2.882854 68.59184 at 30iterations 1.641732 37.38874 at 40iterations 0.9295005 21.78496 at 50iterations 0.5251566 11.25201 at 60iterations 0.2961340 7.013189 at 70iterations 0.1670146 3.533214 at 80iterations 9.3862101E-02 2.028416 at 90iterations 5.2801121E-02 1.057693 at 100iterations 2.9671984E-02 0.7355576 at 110iterations 1.6657973E-02 0.3401041 at 120iterations 9.3678264E-03 0.1805077 at 130iterations 5.2583907E-03 0.1016479 at 140iterations 2.9577939E-03 6.0234070E-02 at 150iterations 1.6708036E-03 3.1231403E-02 at 160iterations 9.4081141E-04 1.9729614E-02 at 170iterations 5.3483824E-04 1.0840774E-02 at 180iterations finished qdiffx linear iterations at : 18:48:18 total time elapsed so far: 11.70000 # loops : 180 mean,max change (kT/e) : 5.3483824E-04 1.0840774E-02 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.88000 DelPhi exited at 18:48:19 11.883u 0.271s 0:12.47 97.4% 0+0k 0+0io 0pf+0w