Mon Oct 10 14:16:35 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 14:16:35 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3032 !!! WARNING: ADP 667 has a net charge of -2.0000 !!! WARNING: MG6 669 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5699648 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): -16.20200 46.25800 ymin,ymax (A): -48.31200 13.88000 zmin,zma (A): -9.491000 42.58400 x,y,z range (A): 62.46000 62.19200 52.07500 scale (grids/A): 0.5699648 object centre (A): 15.02800 -17.21600 16.54650 number of atom coordinates read : 3032 total number of charged atoms : 2888 net assigned charge : 1.400008 assigned positive charge : 476.5900 centred at (gu) : 88.38739 90.22697 89.41633 assigned negative charge : -475.1910 centred at (gu) : 88.42334 90.12727 89.50316 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6509 nv = 96 ne = 84 npr = 58876 no. pairs analyzed = 58876 no. exposed pairs = 4173 no. arc points = 29446 no. surface atoms = 1397 nbur = 1635 mkacc time = 0.1300000 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 = 1.540000 m= 304 mr = 3203 m= 4 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3053 ## 360 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8398 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8746606E-09 -1.1081186E-09 midg,1,midg; midg,igrid,midg -1.4168511E-09 1.9420470E-09 1,midg,midg; igrid,midg,midg 1.1653678E-09 -2.7796435E-10 gauss-seidel spectral radius is 0.9841260 estimated iterations to convergence 65 setup time was (sec) 0.5400000 now iterating at: 14:16:36 rms-change max change #iterations 9.4683342E-02 14.91418 at 10iterations 6.9871619E-03 1.289498 at 20iterations 5.2143703E-04 7.9704285E-02 at 30iterations 4.1049116E-05 6.8531036E-03 at 40iterations 3.9547581E-06 5.3024292E-04 at 50iterations finished qdiffx linear iterations at : 14:16:38 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 3.9547581E-06 5.3024292E-04 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 14:16:39 3.216u 0.161s 0:03.78 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 14:16:39 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3032 !!! WARNING: ADP 667 has a net charge of -2.0000 !!! WARNING: MG6 669 has a net charge of 1.4000 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: 1.709894 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): -16.20200 46.25800 ymin,ymax (A): -48.31200 13.88000 zmin,zma (A): -9.491000 42.58400 x,y,z range (A): 62.46000 62.19200 52.07500 scale (grids/A): 1.709894 object centre (A): 15.02800 -17.21600 16.54650 number of atom coordinates read : 3032 total number of charged atoms : 2888 net assigned charge : 1.400008 assigned positive charge : 476.5900 centred at (gu) : 85.16138 90.68015 88.24830 assigned negative charge : -475.1910 centred at (gu) : 85.26973 90.38145 88.50917 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29446 grid for indexing accessible points = 1.400000 m= 22565 mr = 46739 m= 2610 mr = 14980 m= 72 mr = 1216 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 33343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 282 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 22317 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) : 0.5699648 object centre at (A) : 15.02800 -17.21600 16.54650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2746646E-03 -2.1547465E-02 midg,1,midg; midg,igrid,midg -3.8803869E-03 1.5222684E-02 1,midg,midg; igrid,midg,midg 2.2864489E-02 9.5521687E-03 gauss-seidel spectral radius is 0.9983704 estimated iterations to convergence 197 setup time was (sec) 0.8100000 now iterating at: 14:16:40 rms-change max change #iterations 3.834046 158.7915 at 10iterations 1.658688 61.86503 at 20iterations 0.7222031 26.97427 at 30iterations 0.3135424 10.51122 at 40iterations 0.1366945 4.789976 at 50iterations 5.9680939E-02 2.112517 at 60iterations 2.5991561E-02 0.8737125 at 70iterations 1.1392057E-02 0.3938103 at 80iterations 4.9545495E-03 0.1758757 at 90iterations 2.1595929E-03 7.7234268E-02 at 100iterations 9.4504224E-04 3.5392761E-02 at 110iterations 4.1482536E-04 1.4347076E-02 at 120iterations finished qdiffx linear iterations at : 14:16:47 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 4.1482536E-04 1.4347076E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 14:16:47 7.630u 0.289s 0:08.36 94.6% 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 14:16:47 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3032 !!! WARNING: ADP 667 has a net charge of -2.0000 !!! WARNING: MG6 669 has a net charge of 1.4000 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: 2.564841 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): -16.20200 46.25800 ymin,ymax (A): -48.31200 13.88000 zmin,zma (A): -9.491000 42.58400 x,y,z range (A): 62.46000 62.19200 52.07500 scale (grids/A): 2.564841 object centre (A): 15.02800 -17.21600 16.54650 number of atom coordinates read : 3032 total number of charged atoms : 2888 net assigned charge : 1.400008 assigned positive charge : 476.5900 centred at (gu) : 82.74187 91.02002 87.37230 assigned negative charge : -475.1910 centred at (gu) : 82.90456 90.57198 87.76366 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 164763 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29446 grid for indexing accessible points = 1.400000 m= 76314 mr = 115183 m= 23095 mr = 58678 m= 4095 mr = 16998 m= 294 mr = 2499 m= 11 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 75107 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 23089 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) : 1.709894 object centre at (A) : 15.02800 -17.21600 16.54650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4788508E-02 -0.3421769 midg,1,midg; midg,igrid,midg -4.4598322E-02 9.3511708E-02 1,midg,midg; igrid,midg,midg 0.3406924 6.9888256E-02 gauss-seidel spectral radius is 0.9992013 estimated iterations to convergence 279 setup time was (sec) 1.600000 now iterating at: 14:16:49 rms-change max change #iterations 9.718198 299.2484 at 10iterations 5.631941 135.4494 at 20iterations 3.237436 74.25694 at 30iterations 1.846698 39.37638 at 40iterations 1.051635 21.91026 at 50iterations 0.5972984 13.51258 at 60iterations 0.3387088 7.147542 at 70iterations 0.1914243 3.674781 at 80iterations 0.1081868 2.401633 at 90iterations 6.1159909E-02 1.371547 at 100iterations 3.4513295E-02 0.6643543 at 110iterations 1.9393574E-02 0.4036680 at 120iterations 1.0942267E-02 0.2095032 at 130iterations 6.1622667E-03 0.1231995 at 140iterations 3.4659717E-03 6.7608833E-02 at 150iterations 1.9482315E-03 4.1664124E-02 at 160iterations 1.0977152E-03 2.1631241E-02 at 170iterations 6.1635801E-04 1.1103630E-02 at 180iterations finished qdiffx linear iterations at : 14:17:01 total time elapsed so far: 13.77000 # loops : 180 mean,max change (kT/e) : 6.1635801E-04 1.1103630E-02 energy calculations done at 13.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.94000 DelPhi exited at 14:17:02 13.943u 0.305s 0:14.86 95.8% 0+0k 0+0io 0pf+0w