Sat Oct 8 11:35:16 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 Sat Oct 8 2011 at 11:35:16 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3177 !!! WARNING: HIT 128 has a net charge of 0.5140 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: 0.5655552 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): -14.35300 48.59400 ymin,ymax (A): -38.30300 23.26600 zmin,zma (A): -51.45200 11.11600 x,y,z range (A): 62.94700 61.56900 62.56800 scale (grids/A): 0.5655552 object centre (A): 17.12050 -7.518500 -20.16800 number of atom coordinates read : 3177 total number of charged atoms : 3019 net assigned charge : -3.985987 assigned positive charge : 477.6444 centred at (gu) : 88.41117 91.72829 89.55206 assigned negative charge : -481.6319 centred at (gu) : 88.37017 91.72150 89.59350 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6860 nv = 96 ne = 84 npr = 60824 no. pairs analyzed = 60824 no. exposed pairs = 4462 no. arc points = 32700 no. surface atoms = 1500 nbur = 1677 mkacc time = 0.1600000 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 = 1.512000 m= 295 mr = 3192 m= 0 mr = 8 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3272 ## 401 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8683 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9555669E-11 -1.0022800E-09 midg,1,midg; midg,igrid,midg -4.0869344E-10 -6.1571470E-10 1,midg,midg; igrid,midg,midg -1.6251918E-09 4.8177757E-11 gauss-seidel spectral radius is 0.9839044 estimated iterations to convergence 65 setup time was (sec) 0.6300000 now iterating at: 11:35:17 rms-change max change #iterations 9.2270970E-02 13.61822 at 10iterations 6.8468568E-03 1.164390 at 20iterations 5.0735165E-04 8.9130402E-02 at 30iterations 5.1589192E-05 1.0192871E-02 at 40iterations 8.9498617E-06 1.8386841E-03 at 50iterations finished qdiffx linear iterations at : 11:35:21 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 8.9498617E-06 1.8386841E-03 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 11:35:21 4.512u 0.423s 0:05.23 94.2% 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 Sat Oct 8 2011 at 11:35:22 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3177 !!! WARNING: HIT 128 has a net charge of 0.5140 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: 1.696665 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): -14.35300 48.59400 ymin,ymax (A): -38.30300 23.26600 zmin,zma (A): -51.45200 11.11600 x,y,z range (A): 62.94700 61.56900 62.56800 scale (grids/A): 1.696665 object centre (A): 17.12050 -7.518500 -20.16800 number of atom coordinates read : 3177 total number of charged atoms : 3019 net assigned charge : -3.985987 assigned positive charge : 477.6444 centred at (gu) : 85.23249 95.18370 88.65544 assigned negative charge : -481.6319 centred at (gu) : 85.11043 95.16394 88.78007 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 74796 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32700 grid for indexing accessible points = 1.400000 m= 21975 mr = 47261 m= 2159 mr = 14187 m= 60 mr = 914 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 514 time to turn everything in is 0.6100000 number of dielectric boundary points 36628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 375 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 23305 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) : 0.5655552 object centre at (A) : 17.12050 -7.518500 -20.16800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9513009E-02 2.1093858E-03 midg,1,midg; midg,igrid,midg -6.6051451E-03 4.0657814E-03 1,midg,midg; igrid,midg,midg -1.3609759E-02 8.5588107E-03 gauss-seidel spectral radius is 0.9983643 estimated iterations to convergence 196 setup time was (sec) 0.9600000 now iterating at: 11:35:23 rms-change max change #iterations 3.804572 165.6668 at 10iterations 1.648935 64.08179 at 20iterations 0.7154390 25.49493 at 30iterations 0.3114559 10.23007 at 40iterations 0.1352550 4.534069 at 50iterations 5.8772720E-02 2.127467 at 60iterations 2.5610011E-02 0.8205585 at 70iterations 1.1140884E-02 0.4196769 at 80iterations 4.8481724E-03 0.1616898 at 90iterations 2.1038055E-03 7.3532104E-02 at 100iterations 9.1841165E-04 3.4393311E-02 at 110iterations 4.0050581E-04 1.4427185E-02 at 120iterations finished qdiffx linear iterations at : 11:35:33 total time elapsed so far: 10.67000 # loops : 120 mean,max change (kT/e) : 4.0050581E-04 1.4427185E-02 energy calculations done at 10.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.83000 DelPhi exited at 11:35:33 10.837u 0.474s 0:11.67 96.8% 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 Sat Oct 8 2011 at 11:35:33 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3177 !!! WARNING: HIT 128 has a net charge of 0.5140 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: 2.544998 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): -14.35300 48.59400 ymin,ymax (A): -38.30300 23.26600 zmin,zma (A): -51.45200 11.11600 x,y,z range (A): 62.94700 61.56900 62.56800 scale (grids/A): 2.544998 object centre (A): 17.12050 -7.518500 -20.16800 number of atom coordinates read : 3177 total number of charged atoms : 3019 net assigned charge : -3.985987 assigned positive charge : 477.6444 centred at (gu) : 82.84863 97.77544 87.98289 assigned negative charge : -481.6319 centred at (gu) : 82.66540 97.74594 88.16994 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 173386 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32700 grid for indexing accessible points = 1.400000 m= 75649 mr = 116545 m= 21342 mr = 57482 m= 3240 mr = 15219 m= 202 mr = 1905 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 1699 time to turn everything in is 1.510000 number of dielectric boundary points 82612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 24133 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) : 1.696665 object centre at (A) : 17.12050 -7.518500 -20.16800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5207043 0.3843020 midg,1,midg; midg,igrid,midg -0.1063853 6.2099703E-02 1,midg,midg; igrid,midg,midg -0.1558743 8.6203337E-02 gauss-seidel spectral radius is 0.9992174 estimated iterations to convergence 282 setup time was (sec) 1.840000 now iterating at: 11:35:36 rms-change max change #iterations 9.827290 376.1783 at 10iterations 5.763353 142.9238 at 20iterations 3.328911 80.33463 at 30iterations 1.919922 43.91946 at 40iterations 1.102320 25.01786 at 50iterations 0.6314462 13.84540 at 60iterations 0.3597464 8.246927 at 70iterations 0.2048957 4.633643 at 80iterations 0.1164864 2.380937 at 90iterations 6.6125005E-02 1.441603 at 100iterations 3.7503555E-02 0.7907410 at 110iterations 2.1211568E-02 0.4453959 at 120iterations 1.2048129E-02 0.2324820 at 130iterations 6.8053450E-03 0.1239395 at 140iterations 3.8528203E-03 7.6570511E-02 at 150iterations 2.1812546E-03 4.1814804E-02 at 160iterations 1.2328087E-03 2.9561996E-02 at 170iterations 7.0041040E-04 1.4991760E-02 at 180iterations finished qdiffx linear iterations at : 11:35:52 total time elapsed so far: 17.98000 # loops : 180 mean,max change (kT/e) : 7.0041040E-04 1.4991760E-02 energy calculations done at 17.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.15000 DelPhi exited at 11:35:52 18.158u 0.487s 0:19.15 97.2% 0+0k 0+0io 0pf+0w