Tue Oct 11 03:23:22 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 03:23:22 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1167 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7355067 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): -6.374000 30.50400 ymin,ymax (A): 1.321000 39.65300 zmin,zma (A): -2.365000 46.03700 x,y,z range (A): 36.87800 38.33200 48.40200 scale (grids/A): 0.7355067 object centre (A): 12.06500 20.48700 21.83600 number of atom coordinates read : 1167 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.7231 centred at (gu) : 89.06019 89.31448 88.64262 assigned negative charge : -170.2231 centred at (gu) : 88.73911 89.30450 88.65567 start vw surface at 5.9999999E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4333 nv = 96 ne = 84 npr = 22460 no. pairs analyzed = 22460 no. exposed pairs = 1474 no. arc points = 11065 no. surface atoms = 499 nbur = 668 mkacc time = 4.0000003E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 272 mr = 2238 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 5.0000001E-02 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.1100000 number of dielectric boundary points 2322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 908 ## 72 charges are in solution ## iepsmp to db, and charging done at 0.1700000 number of grid points assigned charge 4434 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2310340E-07 6.5190271E-08 midg,1,midg; midg,igrid,midg 9.5844406E-08 8.3402327E-08 1,midg,midg; igrid,midg,midg -8.8978190E-08 2.0325456E-07 gauss-seidel spectral radius is 0.9902728 estimated iterations to convergence 82 setup time was (sec) 0.2900000 now iterating at: 03:23:22 rms-change max change #iterations 0.1700546 30.30722 at 10iterations 2.2629762E-02 3.667379 at 20iterations 2.9309886E-03 0.5229301 at 30iterations 3.7696835E-04 6.7718506E-02 at 40iterations 4.9872629E-05 8.4037781E-03 at 50iterations finished qdiffx linear iterations at : 03:23:25 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 4.9872629E-05 8.4037781E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 03:23:26 3.271u 0.188s 0:03.90 88.4% 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 03:23:26 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1167 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.206520 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): -6.374000 30.50400 ymin,ymax (A): 1.321000 39.65300 zmin,zma (A): -2.365000 46.03700 x,y,z range (A): 36.87800 38.33200 48.40200 scale (grids/A): 2.206520 object centre (A): 12.06500 20.48700 21.83600 number of atom coordinates read : 1167 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.7231 centred at (gu) : 87.18063 87.94350 85.92799 assigned negative charge : -170.2231 centred at (gu) : 86.21750 87.91363 85.96715 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 45107 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11065 grid for indexing accessible points = 1.400000 m= 17045 mr = 29375 m= 3389 mr = 12683 m= 330 mr = 2275 m= 4 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 1477 time to turn everything in is 0.2400000 number of dielectric boundary points 21373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8445 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) : 0.7355067 object centre at (A) : 12.06500 20.48700 21.83600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2058176E-02 3.4017186E-03 midg,1,midg; midg,igrid,midg 3.8138177E-02 3.2330558E-02 1,midg,midg; igrid,midg,midg -2.6786732E-02 4.1223567E-02 gauss-seidel spectral radius is 0.9988242 estimated iterations to convergence 231 setup time was (sec) 0.4500000 now iterating at: 03:23:26 rms-change max change #iterations 3.573546 212.3416 at 10iterations 1.760018 84.90049 at 20iterations 0.8658798 36.21235 at 30iterations 0.4279566 16.64393 at 40iterations 0.2116227 7.355975 at 50iterations 0.1044199 4.110912 at 60iterations 5.1416170E-02 2.022890 at 70iterations 2.5320459E-02 0.9586906 at 80iterations 1.2475528E-02 0.4373279 at 90iterations 6.1558932E-03 0.2445726 at 100iterations 3.0358562E-03 0.1122570 at 110iterations 1.4996422E-03 5.4718018E-02 at 120iterations finished qdiffx linear iterations at : 03:23:33 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 1.4996422E-03 5.4718018E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 03:23:34 7.519u 0.223s 0:08.27 93.4% 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 03:23:34 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1167 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.309780 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): -6.374000 30.50400 ymin,ymax (A): 1.321000 39.65300 zmin,zma (A): -2.365000 46.03700 x,y,z range (A): 36.87800 38.33200 48.40200 scale (grids/A): 3.309780 object centre (A): 12.06500 20.48700 21.83600 number of atom coordinates read : 1167 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.7231 centred at (gu) : 85.77100 86.91523 83.89202 assigned negative charge : -170.2231 centred at (gu) : 84.32619 86.87045 83.95076 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 103730 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11065 grid for indexing accessible points = 1.400000 m= 52081 mr = 70915 m= 21716 mr = 42536 m= 6397 mr = 17812 m= 1323 mr = 4956 m= 145 mr = 1019 m= 4 mr = 95 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 4657 time to turn everything in is 0.7100000 number of dielectric boundary points 48064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 8488 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) : 2.206520 object centre at (A) : 12.06500 20.48700 21.83600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1339347 -1.5734795E-03 midg,1,midg; midg,igrid,midg 0.3314942 0.2724546 1,midg,midg; igrid,midg,midg -0.2132625 0.3004340 gauss-seidel spectral radius is 0.9992889 estimated iterations to convergence 296 setup time was (sec) 0.9300000 now iterating at: 03:23:35 rms-change max change #iterations 7.789843 314.5240 at 10iterations 4.522129 114.1044 at 20iterations 2.611800 56.73310 at 30iterations 1.514183 34.43903 at 40iterations 0.8736353 19.90071 at 50iterations 0.5052856 11.25768 at 60iterations 0.2928623 6.328182 at 70iterations 0.1691457 3.516739 at 80iterations 9.8042034E-02 2.034773 at 90iterations 5.6601286E-02 1.284973 at 100iterations 3.2751344E-02 0.7485886 at 110iterations 1.9017171E-02 0.4048862 at 120iterations 1.0954816E-02 0.2356784 at 130iterations 6.3544367E-03 0.1403275 at 140iterations 3.6774122E-03 7.7075958E-02 at 150iterations 2.1295976E-03 4.7500610E-02 at 160iterations 1.2354563E-03 2.6949048E-02 at 170iterations 7.1481557E-04 1.5497208E-02 at 180iterations finished qdiffx linear iterations at : 03:23:46 total time elapsed so far: 11.76000 # loops : 180 mean,max change (kT/e) : 7.1481557E-04 1.5497208E-02 energy calculations done at 11.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.89000 DelPhi exited at 03:23:46 11.891u 0.197s 0:12.37 97.6% 0+0k 0+0io 0pf+0w