Mon Oct 10 19:33:12 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+sph2.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 = amb2.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 19:33:12 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2560 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: 0.5411980 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): -6.076000 43.83200 ymin,ymax (A): 1.438000 67.21800 zmin,zma (A): -19.20200 29.23500 x,y,z range (A): 49.90800 65.78000 48.43700 scale (grids/A): 0.5411980 object centre (A): 18.87800 34.32800 5.016500 number of atom coordinates read : 2560 total number of charged atoms : 2387 net assigned charge : 7.000017 assigned positive charge : 375.1399 centred at (gu) : 89.84808 89.56528 90.74776 assigned negative charge : -368.1408 centred at (gu) : 89.71677 89.74139 90.77102 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4997 nv = 96 ne = 84 npr = 50521 no. pairs analyzed = 50521 no. exposed pairs = 3496 no. arc points = 25468 no. surface atoms = 1177 nbur = 1383 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 = 1.596000 m= 209 mr = 2388 m= 0 mr = 6 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2506 ## 387 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6372 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8883008E-10 3.0203734E-10 midg,1,midg; midg,igrid,midg 1.2839199E-09 -4.1710252E-10 1,midg,midg; igrid,midg,midg -2.6419700E-10 9.1797070E-10 gauss-seidel spectral radius is 0.9823771 estimated iterations to convergence 62 setup time was (sec) 0.5600000 now iterating at: 19:33:13 rms-change max change #iterations 6.4919412E-02 15.13685 at 10iterations 4.1829287E-03 0.6842442 at 20iterations 2.8774791E-04 4.9695969E-02 at 30iterations 2.1591841E-05 3.7689209E-03 at 40iterations 2.1621422E-06 4.1198730E-04 at 50iterations finished qdiffx linear iterations at : 19:33:17 total time elapsed so far: 4.450000 # loops : 50 mean,max change (kT/e) : 2.1621422E-06 4.1198730E-04 energy calculations done at 4.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 19:33:17 4.624u 0.378s 0:05.49 90.8% 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 19:33:17 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2560 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: 1.623594 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): -6.076000 43.83200 ymin,ymax (A): 1.438000 67.21800 zmin,zma (A): -19.20200 29.23500 x,y,z range (A): 49.90800 65.78000 48.43700 scale (grids/A): 1.623594 object centre (A): 18.87800 34.32800 5.016500 number of atom coordinates read : 2560 total number of charged atoms : 2387 net assigned charge : 7.000017 assigned positive charge : 375.1399 centred at (gu) : 89.54369 88.69520 92.24272 assigned negative charge : -368.1408 centred at (gu) : 89.15035 89.22404 92.31275 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 54521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25468 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 16595 mr = 35065 m= 1766 mr = 10976 m= 55 mr = 797 m= 1 mr = 1 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 0.4700000 number of dielectric boundary points 26099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 388 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 18270 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) : 0.5411980 object centre at (A) : 18.87800 34.32800 5.016500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1424063E-03 4.2330087E-04 midg,1,midg; midg,igrid,midg 2.0280402E-02 -7.0189834E-03 1,midg,midg; igrid,midg,midg -6.3047558E-03 9.0073589E-03 gauss-seidel spectral radius is 0.9981269 estimated iterations to convergence 184 setup time was (sec) 0.7600000 now iterating at: 19:33:19 rms-change max change #iterations 2.969005 156.8081 at 10iterations 1.220137 53.84137 at 20iterations 0.5007176 19.28885 at 30iterations 0.2059709 7.924219 at 40iterations 8.4429674E-02 3.338763 at 50iterations 3.4572013E-02 1.308307 at 60iterations 1.4260946E-02 0.5636134 at 70iterations 5.8689341E-03 0.2483726 at 80iterations 2.4104908E-03 0.1079226 at 90iterations 9.9074782E-04 4.1187644E-02 at 100iterations 4.0776475E-04 1.6644001E-02 at 110iterations 1.6664113E-04 7.1169138E-03 at 120iterations finished qdiffx linear iterations at : 19:33:29 total time elapsed so far: 10.95000 # loops : 120 mean,max change (kT/e) : 1.6664113E-04 7.1169138E-03 energy calculations done at 10.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.11000 DelPhi exited at 19:33:30 11.112u 0.446s 0:12.30 93.9% 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 Mon Oct 10 2011 at 19:33:30 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2560 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: 2.435391 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): -6.076000 43.83200 ymin,ymax (A): 1.438000 67.21800 zmin,zma (A): -19.20200 29.23500 x,y,z range (A): 49.90800 65.78000 48.43700 scale (grids/A): 2.435391 object centre (A): 18.87800 34.32800 5.016500 number of atom coordinates read : 2560 total number of charged atoms : 2387 net assigned charge : 7.000017 assigned positive charge : 375.1399 centred at (gu) : 89.31535 88.04261 93.36405 assigned negative charge : -368.1408 centred at (gu) : 88.72548 88.83595 93.46924 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 126377 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25468 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 56550 mr = 86261 m= 16327 mr = 43420 m= 2757 mr = 11901 m= 166 mr = 1656 m= 4 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.130000 number of dielectric boundary points 58904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 19068 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) : 1.623594 object centre at (A) : 18.87800 34.32800 5.016500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3203107E-02 -1.2490290E-02 midg,1,midg; midg,igrid,midg 0.3338520 -9.7175367E-02 1,midg,midg; igrid,midg,midg -7.5039074E-02 0.1315768 gauss-seidel spectral radius is 0.9991177 estimated iterations to convergence 266 setup time was (sec) 1.450000 now iterating at: 19:33:32 rms-change max change #iterations 7.773568 318.6746 at 10iterations 4.357600 127.9388 at 20iterations 2.407449 64.09258 at 30iterations 1.330209 34.63166 at 40iterations 0.7297273 18.16982 at 50iterations 0.3991309 10.14005 at 60iterations 0.2185839 5.085309 at 70iterations 0.1195924 2.732840 at 80iterations 6.5156758E-02 1.615692 at 90iterations 3.5553239E-02 0.8718038 at 100iterations 1.9371364E-02 0.4381866 at 110iterations 1.0544550E-02 0.2518806 at 120iterations 5.7443338E-03 0.1237893 at 130iterations 3.1311088E-03 6.6844940E-02 at 140iterations 1.7043991E-03 3.6514282E-02 at 150iterations 9.2810352E-04 2.0023346E-02 at 160iterations 5.0567550E-04 1.0727167E-02 at 170iterations 2.7509526E-04 6.2618256E-03 at 180iterations finished qdiffx linear iterations at : 19:33:48 total time elapsed so far: 17.40000 # loops : 180 mean,max change (kT/e) : 2.7509526E-04 6.2618256E-03 energy calculations done at 17.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.56000 DelPhi exited at 19:33:48 17.560u 0.464s 0:18.59 96.9% 0+0k 0+0io 0pf+0w