Sat Oct 15 12:01:02 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 12:01:02 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 = 2162 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6850896 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): 0.7310001 52.69500 ymin,ymax (A): -15.22300 27.67800 zmin,zma (A): -11.48100 39.68800 x,y,z range (A): 51.96400 42.90100 51.16900 scale (grids/A): 0.6850896 object centre (A): 26.71300 6.227500 14.10350 number of atom coordinates read : 2162 total number of charged atoms : 2028 net assigned charge : 9.500021 assigned positive charge : 313.3449 centred at (gu) : 89.47428 88.58920 91.50230 assigned negative charge : -303.8452 centred at (gu) : 89.48151 88.67805 91.46426 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7023 nv = 96 ne = 84 npr = 43317 no. pairs analyzed = 43317 no. exposed pairs = 2796 no. arc points = 20215 no. surface atoms = 939 nbur = 1223 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 462 mr = 3764 m= 3 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.1700000 number of dielectric boundary points 3653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1858 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7895 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6186804E-08 7.6067231E-08 midg,1,midg; midg,igrid,midg 9.3947804E-08 1.5570109E-08 1,midg,midg; igrid,midg,midg 5.2891554E-08 3.9410594E-08 gauss-seidel spectral radius is 0.9889214 estimated iterations to convergence 77 setup time was (sec) 0.3600000 now iterating at: 12:01:02 rms-change max change #iterations 0.1756711 26.45732 at 10iterations 1.9833110E-02 2.729713 at 20iterations 2.3024376E-03 0.3383904 at 30iterations 2.6854771E-04 3.7200928E-02 at 40iterations 3.0996263E-05 4.1542053E-03 at 50iterations finished qdiffx linear iterations at : 12:01:05 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 3.0996263E-05 4.1542053E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 12:01:06 3.398u 0.195s 0:03.93 91.0% 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 12:01:06 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 = 2162 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.055269 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): 0.7310001 52.69500 ymin,ymax (A): -15.22300 27.67800 zmin,zma (A): -11.48100 39.68800 x,y,z range (A): 51.96400 42.90100 51.16900 scale (grids/A): 2.055269 object centre (A): 26.71300 6.227500 14.10350 number of atom coordinates read : 2162 total number of charged atoms : 2028 net assigned charge : 9.500021 assigned positive charge : 313.3449 centred at (gu) : 88.42273 85.76761 94.50668 assigned negative charge : -303.8452 centred at (gu) : 88.44472 86.03407 94.39286 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20215 grid for indexing accessible points = 1.400000 m= 28119 mr = 49873 m= 5249 mr = 20733 m= 444 mr = 3365 m= 3 mr = 207 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 2318 time to turn everything in is 0.3700000 number of dielectric boundary points 33762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 16071 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) : 0.6850896 object centre at (A) : 26.71300 6.227500 14.10350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7324097E-02 3.8493995E-02 midg,1,midg; midg,igrid,midg 3.2884158E-02 -5.2023497E-03 1,midg,midg; igrid,midg,midg 6.8656787E-02 6.8083741E-02 gauss-seidel spectral radius is 0.9987815 estimated iterations to convergence 227 setup time was (sec) 0.5900000 now iterating at: 12:01:07 rms-change max change #iterations 4.256130 177.9387 at 10iterations 2.066059 80.79253 at 20iterations 1.003976 34.90533 at 30iterations 0.4890355 16.03749 at 40iterations 0.2377771 7.533340 at 50iterations 0.1160160 3.581299 at 60iterations 5.6836706E-02 2.160119 at 70iterations 2.7591133E-02 0.9476779 at 80iterations 1.3427242E-02 0.4196777 at 90iterations 6.5473691E-03 0.2009847 at 100iterations 3.1999818E-03 0.1109848 at 110iterations 1.5638886E-03 4.7704697E-02 at 120iterations finished qdiffx linear iterations at : 12:01:14 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 1.5638886E-03 4.7704697E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 12:01:14 7.961u 0.231s 0:08.56 95.6% 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 Sat Oct 15 2011 at 12:01:14 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 = 2162 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.082904 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): 0.7310001 52.69500 ymin,ymax (A): -15.22300 27.67800 zmin,zma (A): -11.48100 39.68800 x,y,z range (A): 51.96400 42.90100 51.16900 scale (grids/A): 3.082904 object centre (A): 26.71300 6.227500 14.10350 number of atom coordinates read : 2162 total number of charged atoms : 2028 net assigned charge : 9.500021 assigned positive charge : 313.3449 centred at (gu) : 87.63400 83.65138 96.75994 assigned negative charge : -303.8452 centred at (gu) : 87.66710 84.05121 96.58939 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 170872 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20215 grid for indexing accessible points = 1.400000 m= 87805 mr = 120859 m= 35049 mr = 71483 m= 9742 mr = 28194 m= 1807 mr = 7437 m= 138 mr = 1302 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 7513 time to turn everything in is 1.120000 number of dielectric boundary points 76066 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 16220 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) : 2.055269 object centre at (A) : 26.71300 6.227500 14.10350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6994771 0.4002525 midg,1,midg; midg,igrid,midg 0.2705848 -3.6205888E-02 1,midg,midg; igrid,midg,midg 0.5574476 0.7171628 gauss-seidel spectral radius is 0.9993007 estimated iterations to convergence 298 setup time was (sec) 1.360000 now iterating at: 12:01:16 rms-change max change #iterations 9.886062 446.3794 at 10iterations 5.860968 146.3284 at 20iterations 3.469963 77.34361 at 30iterations 2.047527 46.65167 at 40iterations 1.203203 23.90353 at 50iterations 0.7054350 14.11132 at 60iterations 0.4131548 8.939172 at 70iterations 0.2429141 4.819478 at 80iterations 0.1421108 2.597261 at 90iterations 8.3129197E-02 1.464500 at 100iterations 4.8593272E-02 1.001316 at 110iterations 2.8370555E-02 0.5232697 at 120iterations 1.6582040E-02 0.3026733 at 130iterations 9.7245397E-03 0.2038422 at 140iterations 5.6947935E-03 0.1150246 at 150iterations 3.3361055E-03 6.4548492E-02 at 160iterations 1.9571618E-03 3.6830902E-02 at 170iterations 1.1552414E-03 2.3042679E-02 at 180iterations finished qdiffx linear iterations at : 12:01:28 total time elapsed so far: 13.00000 # loops : 180 mean,max change (kT/e) : 1.1552414E-03 2.3042679E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 12:01:28 13.130u 0.232s 0:13.63 98.0% 0+0k 0+0io 0pf+0w