Tue Oct 11 08:37:38 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 Tue Oct 11 2011 at 08:37:38 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 = 2715 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: 0.6632140 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): -15.22300 33.21600 ymin,ymax (A): 7.429000 55.65300 zmin,zma (A): 25.71600 79.39400 x,y,z range (A): 48.43900 48.22400 53.67800 scale (grids/A): 0.6632140 object centre (A): 8.996500 31.54100 52.55500 number of atom coordinates read : 2715 total number of charged atoms : 2567 net assigned charge : 1.500014 assigned positive charge : 411.2377 centred at (gu) : 90.18476 90.49043 88.51741 assigned negative charge : -409.7383 centred at (gu) : 90.42555 90.32595 88.61930 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8025 nv = 96 ne = 84 npr = 55409 no. pairs analyzed = 55409 no. exposed pairs = 3320 no. arc points = 23037 no. surface atoms = 1109 nbur = 1606 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 456 mr = 4605 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3600000 number of dielectric boundary points 3806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2245 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9477 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6401868E-08 -1.4247100E-08 midg,1,midg; midg,igrid,midg -3.0709458E-08 4.4767834E-08 1,midg,midg; igrid,midg,midg 5.4751752E-08 -5.4203088E-08 gauss-seidel spectral radius is 0.9882234 estimated iterations to convergence 75 setup time was (sec) 0.6300000 now iterating at: 08:37:39 rms-change max change #iterations 0.1756371 24.89644 at 10iterations 1.9196125E-02 2.367950 at 20iterations 2.1680405E-03 0.2883759 at 30iterations 2.7323674E-04 3.5652161E-02 at 40iterations 5.1082199E-05 7.0285797E-03 at 50iterations finished qdiffx linear iterations at : 08:37:43 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 5.1082199E-05 7.0285797E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 08:37:43 4.143u 0.288s 0:04.74 93.2% 0+0k 0+0io 6pf+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 08:37:43 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 = 2715 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: 1.989642 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): -15.22300 33.21600 ymin,ymax (A): 7.429000 55.65300 zmin,zma (A): 25.71600 79.39400 x,y,z range (A): 48.43900 48.22400 53.67800 scale (grids/A): 1.989642 object centre (A): 8.996500 31.54100 52.55500 number of atom coordinates read : 2715 total number of charged atoms : 2567 net assigned charge : 1.500014 assigned positive charge : 411.2377 centred at (gu) : 90.55373 91.47066 85.55141 assigned negative charge : -409.7383 centred at (gu) : 91.27622 90.97749 85.85752 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 86311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23037 grid for indexing accessible points = 1.400000 m= 32260 mr = 61364 m= 5256 mr = 24266 m= 344 mr = 3369 m= 8 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 2362 time to turn everything in is 0.7600000 number of dielectric boundary points 35038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 20302 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) : 0.6632140 object centre at (A) : 8.996500 31.54100 52.55500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0662198E-02 -5.7050325E-02 midg,1,midg; midg,igrid,midg -1.7962128E-02 3.2176312E-02 1,midg,midg; igrid,midg,midg 7.6404490E-02 -1.6575614E-02 gauss-seidel spectral radius is 0.9987553 estimated iterations to convergence 224 setup time was (sec) 1.050000 now iterating at: 08:37:44 rms-change max change #iterations 4.768635 218.7109 at 10iterations 2.319345 80.81756 at 20iterations 1.124384 35.11808 at 30iterations 0.5458040 15.97980 at 40iterations 0.2659645 7.822342 at 50iterations 0.1286676 3.608309 at 60iterations 6.2578171E-02 1.768732 at 70iterations 3.0445563E-02 0.8342953 at 80iterations 1.4779082E-02 0.4411688 at 90iterations 7.1527800E-03 0.2020779 at 100iterations 3.4877337E-03 0.1109934 at 110iterations 1.7017489E-03 5.0981522E-02 at 120iterations finished qdiffx linear iterations at : 08:37:53 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 1.7017489E-03 5.0981522E-02 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.820000 DelPhi exited at 08:37:55 9.826u 0.318s 0:11.67 86.8% 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 Tue Oct 11 2011 at 08:37:55 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 = 2715 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: 2.984463 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): -15.22300 33.21600 ymin,ymax (A): 7.429000 55.65300 zmin,zma (A): 25.71600 79.39400 x,y,z range (A): 48.43900 48.22400 53.67800 scale (grids/A): 2.984463 object centre (A): 8.996500 31.54100 52.55500 number of atom coordinates read : 2715 total number of charged atoms : 2567 net assigned charge : 1.500014 assigned positive charge : 411.2377 centred at (gu) : 90.83049 92.20603 83.32703 assigned negative charge : -409.7383 centred at (gu) : 91.91425 91.46620 83.78629 start vw surface at 0.1600000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 199467 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23037 grid for indexing accessible points = 1.400000 m= 103740 mr = 147915 m= 38688 mr = 86056 m= 9700 mr = 31567 m= 1529 mr = 7512 m= 110 mr = 978 m= 5 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 7794 time to turn everything in is 1.990000 number of dielectric boundary points 79159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 20536 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) : 1.989642 object centre at (A) : 8.996500 31.54100 52.55500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3432702 -0.6033229 midg,1,midg; midg,igrid,midg -0.1812829 0.3755048 1,midg,midg; igrid,midg,midg 0.6497392 -0.1331335 gauss-seidel spectral radius is 0.9992837 estimated iterations to convergence 295 setup time was (sec) 2.320000 now iterating at: 08:37:58 rms-change max change #iterations 10.93396 479.0465 at 10iterations 6.424415 153.8178 at 20iterations 3.754810 72.68564 at 30iterations 2.201778 49.75713 at 40iterations 1.288841 22.44984 at 50iterations 0.7518796 12.99063 at 60iterations 0.4383860 9.349130 at 70iterations 0.2554553 4.552652 at 80iterations 0.1486064 2.454866 at 90iterations 8.6587295E-02 1.594637 at 100iterations 5.0444584E-02 0.9205322 at 110iterations 2.9280365E-02 0.5664864 at 120iterations 1.7082881E-02 0.3263826 at 130iterations 9.9773696E-03 0.1611748 at 140iterations 5.8211335E-03 9.5892906E-02 at 150iterations 3.4358713E-03 7.0142746E-02 at 160iterations 2.0366646E-03 3.2814026E-02 at 170iterations 1.2302634E-03 2.2283554E-02 at 180iterations finished qdiffx linear iterations at : 08:38:12 total time elapsed so far: 16.68000 # loops : 180 mean,max change (kT/e) : 1.2302634E-03 2.2283554E-02 energy calculations done at 16.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.85000 DelPhi exited at 08:38:13 16.852u 0.350s 0:17.62 97.6% 0+0k 0+0io 0pf+0w