Tue Oct 11 05:30:16 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 Tue Oct 11 2011 at 05:30:17 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7340509 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): 25.88800 73.11500 ymin,ymax (A): -18.74300 29.75500 zmin,zma (A): 4.175000 46.63700 x,y,z range (A): 47.22700 48.49800 42.46200 scale (grids/A): 0.7340509 object centre (A): 49.50150 5.506001 25.40600 number of atom coordinates read : 2290 total number of charged atoms : 1963 net assigned charge : 5.945010 assigned positive charge : 319.5460 centred at (gu) : 88.91850 90.62132 90.17765 assigned negative charge : -313.6011 centred at (gu) : 89.05283 90.55921 90.25276 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7823 nv = 96 ne = 84 npr = 41625 no. pairs analyzed = 41625 no. exposed pairs = 2570 no. arc points = 17590 no. surface atoms = 884 nbur = 1406 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 565 mr = 4573 m= 4 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3707 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1555 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8254 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5091436E-07 2.4399307E-08 midg,1,midg; midg,igrid,midg 3.1980687E-08 1.6247382E-07 1,midg,midg; igrid,midg,midg 2.5410640E-07 -2.2923393E-08 gauss-seidel spectral radius is 0.9903222 estimated iterations to convergence 83 setup time was (sec) 0.3700000 now iterating at: 05:30:17 rms-change max change #iterations 0.2336922 36.10624 at 10iterations 3.1624667E-02 4.338576 at 20iterations 4.8023197E-03 0.6723938 at 30iterations 1.0420617E-03 0.1185074 at 40iterations 3.2363145E-04 3.3439636E-02 at 50iterations finished qdiffx linear iterations at : 05:30:20 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 3.2363145E-04 3.3439636E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 05:30:21 3.360u 0.175s 0:04.14 85.2% 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 Tue Oct 11 2011 at 05:30:21 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.202153 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): 25.88800 73.11500 ymin,ymax (A): -18.74300 29.75500 zmin,zma (A): 4.175000 46.63700 x,y,z range (A): 47.22700 48.49800 42.46200 scale (grids/A): 2.202153 object centre (A): 49.50150 5.506001 25.40600 number of atom coordinates read : 2290 total number of charged atoms : 1963 net assigned charge : 5.945010 assigned positive charge : 319.5460 centred at (gu) : 86.75562 91.86389 90.53289 assigned negative charge : -313.6011 centred at (gu) : 87.15853 91.67786 90.75836 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 82247 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17590 grid for indexing accessible points = 1.400000 m= 35391 mr = 58895 m= 7733 mr = 27591 m= 829 mr = 5334 m= 32 mr = 421 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 33988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15619 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) : 0.7340509 object centre at (A) : 49.50150 5.506001 25.40600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4972452E-02 3.1093707E-02 midg,1,midg; midg,igrid,midg 4.6461415E-02 4.5406755E-02 1,midg,midg; igrid,midg,midg 5.6246676E-02 -4.9163766E-02 gauss-seidel spectral radius is 0.9989040 estimated iterations to convergence 239 setup time was (sec) 0.6300000 now iterating at: 05:30:22 rms-change max change #iterations 4.949945 240.8762 at 10iterations 2.505442 82.19861 at 20iterations 1.274520 39.27999 at 30iterations 0.6461927 20.69558 at 40iterations 0.3286677 9.524706 at 50iterations 0.1672044 4.959078 at 60iterations 8.4961250E-02 2.702155 at 70iterations 4.3393660E-02 1.400291 at 80iterations 2.2366516E-02 0.6335411 at 90iterations 1.1564386E-02 0.3837624 at 100iterations 6.0782642E-03 0.1690369 at 110iterations 3.2954130E-03 9.3696594E-02 at 120iterations finished qdiffx linear iterations at : 05:30:29 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 3.2954130E-03 9.3696594E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 05:30:29 7.950u 0.251s 0:08.54 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 Tue Oct 11 2011 at 05:30:30 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.303229 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): 25.88800 73.11500 ymin,ymax (A): -18.74300 29.75500 zmin,zma (A): 4.175000 46.63700 x,y,z range (A): 47.22700 48.49800 42.46200 scale (grids/A): 3.303229 object centre (A): 49.50150 5.506001 25.40600 number of atom coordinates read : 2290 total number of charged atoms : 1963 net assigned charge : 5.945010 assigned positive charge : 319.5460 centred at (gu) : 85.13348 92.79580 90.79938 assigned negative charge : -313.6011 centred at (gu) : 85.73773 92.51694 91.13766 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 189202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17590 grid for indexing accessible points = 1.400000 m= 107403 mr = 141317 m= 47314 mr = 90569 m= 14825 mr = 39731 m= 3338 mr = 11712 m= 474 mr = 2441 m= 38 mr = 303 m= 0 mr = 12 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 76509 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 15704 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) : 2.202153 object centre at (A) : 49.50150 5.506001 25.40600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1388204 0.2481898 midg,1,midg; midg,igrid,midg 0.3643640 0.3284734 1,midg,midg; igrid,midg,midg 0.4893022 -0.5526496 gauss-seidel spectral radius is 0.9993175 estimated iterations to convergence 302 setup time was (sec) 1.600000 now iterating at: 05:30:32 rms-change max change #iterations 10.83785 429.1132 at 10iterations 6.505991 148.5455 at 20iterations 3.885745 81.18678 at 30iterations 2.322162 43.69534 at 40iterations 1.382972 25.41584 at 50iterations 0.8209884 15.11063 at 60iterations 0.4864013 8.345609 at 70iterations 0.2878275 5.394693 at 80iterations 0.1706877 3.035820 at 90iterations 0.1012125 1.685043 at 100iterations 6.0112819E-02 0.9853072 at 110iterations 3.5949878E-02 0.6258392 at 120iterations 2.1751825E-02 0.4082451 at 130iterations 1.3460342E-02 0.2597580 at 140iterations 8.6082565E-03 0.1711502 at 150iterations 5.7973675E-03 0.1091995 at 160iterations 4.1487440E-03 8.4403992E-02 at 170iterations 3.1517283E-03 5.9577942E-02 at 180iterations finished qdiffx linear iterations at : 05:30:44 total time elapsed so far: 13.50000 # loops : 180 mean,max change (kT/e) : 3.1517283E-03 5.9577942E-02 energy calculations done at 13.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.64000 DelPhi exited at 05:30:44 13.640u 0.214s 0:14.41 96.1% 0+0k 0+0io 0pf+0w