Sun Oct 9 21:53:07 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 Sun Oct 9 2011 at 21:53:07 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3161 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 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: 0.6614887 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): 45.36100 98.23600 ymin,ymax (A): 3.472000 57.29000 zmin,zma (A): 15.14700 68.21400 x,y,z range (A): 52.87500 53.81800 53.06699 scale (grids/A): 0.6614887 object centre (A): 71.79850 30.38100 41.68050 number of atom coordinates read : 3161 total number of charged atoms : 3011 net assigned charge : 7.325009 assigned positive charge : 483.6308 centred at (gu) : 90.52087 88.42207 90.74829 assigned negative charge : -476.3071 centred at (gu) : 90.44297 88.35600 90.74241 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 9515 nv = 96 ne = 84 npr = 62278 no. pairs analyzed = 62278 no. exposed pairs = 4086 no. arc points = 29139 no. surface atoms = 1366 nbur = 1795 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 526 mr = 5121 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3200000 number of dielectric boundary points 4865 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2781 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 11066 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5534427E-08 2.4400718E-08 midg,1,midg; midg,igrid,midg 3.3745824E-09 2.6103983E-08 1,midg,midg; igrid,midg,midg -1.1273148E-10 4.3348756E-08 gauss-seidel spectral radius is 0.9882147 estimated iterations to convergence 75 setup time was (sec) 0.5200000 now iterating at: 21:53:08 rms-change max change #iterations 0.1908731 23.41258 at 10iterations 2.0428125E-02 2.566078 at 20iterations 2.2024927E-03 0.2649155 at 30iterations 2.3496449E-04 3.3425331E-02 at 40iterations 2.5515119E-05 3.2272339E-03 at 50iterations finished qdiffx linear iterations at : 21:53:10 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 2.5515119E-05 3.2272339E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 21:53:11 3.145u 0.152s 0:03.59 91.6% 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 Sun Oct 9 2011 at 21:53:11 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3161 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 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: 1.984466 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): 45.36100 98.23600 ymin,ymax (A): 3.472000 57.29000 zmin,zma (A): 15.14700 68.21400 x,y,z range (A): 52.87500 53.81800 53.06699 scale (grids/A): 1.984466 object centre (A): 71.79850 30.38100 41.68050 number of atom coordinates read : 3161 total number of charged atoms : 3011 net assigned charge : 7.325009 assigned positive charge : 483.6308 centred at (gu) : 91.56139 85.26521 92.24411 assigned negative charge : -476.3071 centred at (gu) : 91.32861 85.06763 92.22691 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 101781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29139 grid for indexing accessible points = 1.400000 m= 36853 mr = 70030 m= 6242 mr = 26699 m= 472 mr = 3794 m= 10 mr = 168 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1028 time to turn everything in is 0.6500000 number of dielectric boundary points 44668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 23788 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) : 0.6614887 object centre at (A) : 71.79850 30.38100 41.68050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6278071E-04 -2.0337462E-02 midg,1,midg; midg,igrid,midg 9.2151716E-02 6.3049294E-02 1,midg,midg; igrid,midg,midg 7.6982928E-03 3.9492477E-02 gauss-seidel spectral radius is 0.9987993 estimated iterations to convergence 228 setup time was (sec) 0.9300000 now iterating at: 21:53:12 rms-change max change #iterations 5.184950 182.4222 at 10iterations 2.539532 77.29004 at 20iterations 1.239878 41.35078 at 30iterations 0.6095790 17.10543 at 40iterations 0.2982327 9.532343 at 50iterations 0.1467713 3.967712 at 60iterations 7.1952179E-02 2.000359 at 70iterations 3.5301737E-02 0.9256973 at 80iterations 1.7297952E-02 0.4643669 at 90iterations 8.4968023E-03 0.2259388 at 100iterations 4.1735303E-03 0.1150503 at 110iterations 2.0431830E-03 5.7975769E-02 at 120iterations finished qdiffx linear iterations at : 21:53:18 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 2.0431830E-03 5.7975769E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 21:53:19 7.592u 0.188s 0:08.11 95.8% 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 Sun Oct 9 2011 at 21:53:19 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3161 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 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: 2.976699 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): 45.36100 98.23600 ymin,ymax (A): 3.472000 57.29000 zmin,zma (A): 15.14700 68.21400 x,y,z range (A): 52.87500 53.81800 53.06699 scale (grids/A): 2.976699 object centre (A): 71.79850 30.38100 41.68050 number of atom coordinates read : 3161 total number of charged atoms : 3011 net assigned charge : 7.325009 assigned positive charge : 483.6308 centred at (gu) : 92.34200 82.89769 93.36610 assigned negative charge : -476.3071 centred at (gu) : 91.99285 82.60139 93.34055 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 235105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29139 grid for indexing accessible points = 1.400000 m= 118128 mr = 169585 m= 43813 mr = 95937 m= 11441 mr = 34574 m= 2036 mr = 8437 m= 177 mr = 1373 m= 0 mr = 82 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 3169 time to turn everything in is 1.750000 number of dielectric boundary points 100712 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 24088 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) : 1.984466 object centre at (A) : 71.79850 30.38100 41.68050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5956934E-02 -0.4694488 midg,1,midg; midg,igrid,midg 0.7539688 0.5973884 1,midg,midg; igrid,midg,midg 0.2808338 0.5364820 gauss-seidel spectral radius is 0.9993237 estimated iterations to convergence 303 setup time was (sec) 2.060000 now iterating at: 21:53:21 rms-change max change #iterations 12.01987 410.0005 at 10iterations 7.270772 152.3087 at 20iterations 4.353957 89.56743 at 30iterations 2.604508 45.35960 at 40iterations 1.556704 25.57806 at 50iterations 0.9276330 16.86514 at 60iterations 0.5507694 9.559175 at 70iterations 0.3267773 5.346307 at 80iterations 0.1933002 3.179226 at 90iterations 0.1143814 1.708792 at 100iterations 6.7734987E-02 1.210983 at 110iterations 4.0015019E-02 0.6602478 at 120iterations 2.3673669E-02 0.4140415 at 130iterations 1.3961677E-02 0.2382183 at 140iterations 8.2515040E-03 0.1384277 at 150iterations 4.8655299E-03 8.0169916E-02 at 160iterations 2.8688272E-03 4.4225693E-02 at 170iterations 1.6988823E-03 2.8305054E-02 at 180iterations finished qdiffx linear iterations at : 21:53:31 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 1.6988823E-03 2.8305054E-02 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 21:53:32 12.379u 0.184s 0:12.83 97.8% 0+0k 0+0io 0pf+0w