Mon Oct 10 11:02:57 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 Mon Oct 10 2011 at 11:02:57 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 = 5346 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5099921 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): -29.76300 40.04200 ymin,ymax (A): -28.15100 41.43400 zmin,zma (A): -34.17900 27.27200 x,y,z range (A): 69.80500 69.58501 61.45100 scale (grids/A): 0.5099921 object centre (A): 5.139500 6.641500 -3.453501 number of atom coordinates read : 5346 total number of charged atoms : 5190 net assigned charge : 10.00004 assigned positive charge : 843.9109 centred at (gu) : 89.91611 90.00089 89.99071 assigned negative charge : -833.9188 centred at (gu) : 89.90884 89.95183 90.01520 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8932 nv = 96 ne = 84 npr = 105232 no. pairs analyzed = 105232 no. exposed pairs = 6431 no. arc points = 44317 no. surface atoms = 2170 nbur = 3176 mkacc time = 0.2400000 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 = 1.680000 m= 303 mr = 4887 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.5200000 number of dielectric boundary points 4338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4402 ## 676 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 11884 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1084350E-10 6.5455537E-11 midg,1,midg; midg,igrid,midg -7.6995146E-12 2.8228408E-10 1,midg,midg; igrid,midg,midg 1.1921944E-10 1.5625636E-10 gauss-seidel spectral radius is 0.9803747 estimated iterations to convergence 59 setup time was (sec) 0.7700000 now iterating at: 11:02:58 rms-change max change #iterations 7.0933945E-02 9.985600 at 10iterations 4.2276010E-03 0.6710320 at 20iterations 6.6564698E-04 9.8714828E-02 at 30iterations 3.3721200E-04 4.8913717E-02 at 40iterations 1.8209893E-04 2.6736259E-02 at 50iterations finished qdiffx linear iterations at : 11:03:01 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 1.8209893E-04 2.6736259E-02 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 11:03:02 3.752u 0.208s 0:04.24 93.1% 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 Mon Oct 10 2011 at 11:03:02 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 = 5346 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.529976 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): -29.76300 40.04200 ymin,ymax (A): -28.15100 41.43400 zmin,zma (A): -34.17900 27.27200 x,y,z range (A): 69.80500 69.58501 61.45100 scale (grids/A): 1.529976 object centre (A): 5.139500 6.641500 -3.453501 number of atom coordinates read : 5346 total number of charged atoms : 5190 net assigned charge : 10.00004 assigned positive charge : 843.9109 centred at (gu) : 89.74687 90.00113 89.97046 assigned negative charge : -833.9188 centred at (gu) : 89.72641 89.85538 90.04541 start vw surface at 0.2500000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 101560 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44317 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 30077 mr = 71942 m= 2665 mr = 20700 m= 50 mr = 1166 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 2090 time to turn everything in is 0.7600000 number of dielectric boundary points 40544 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 622 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 38878 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) : 0.5099921 object centre at (A) : 5.139500 6.641500 -3.453501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8625040E-03 1.3189726E-03 midg,1,midg; midg,igrid,midg -1.7843215E-02 1.3952133E-02 1,midg,midg; igrid,midg,midg -9.8344442E-03 2.1655057E-02 gauss-seidel spectral radius is 0.9981574 estimated iterations to convergence 185 setup time was (sec) 1.050000 now iterating at: 11:03:03 rms-change max change #iterations 4.138660 176.2976 at 10iterations 1.713867 53.05335 at 20iterations 0.7126119 22.07428 at 30iterations 0.2968535 8.968122 at 40iterations 0.1231435 3.756369 at 50iterations 5.1309321E-02 1.520735 at 60iterations 2.1377889E-02 0.6863136 at 70iterations 9.0141734E-03 0.2738628 at 80iterations 3.8752747E-03 0.1339645 at 90iterations 1.8089783E-03 6.3156128E-02 at 100iterations 9.9874567E-04 3.4309387E-02 at 110iterations 6.7108870E-04 2.3062229E-02 at 120iterations finished qdiffx linear iterations at : 11:03:10 total time elapsed so far: 8.680000 # loops : 120 mean,max change (kT/e) : 6.7108870E-04 2.3062229E-02 energy calculations done at 8.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.870000 DelPhi exited at 11:03:11 8.869u 0.171s 0:09.33 96.7% 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 Mon Oct 10 2011 at 11:03:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5346 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.294965 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): -29.76300 40.04200 ymin,ymax (A): -28.15100 41.43400 zmin,zma (A): -34.17900 27.27200 x,y,z range (A): 69.80500 69.58501 61.45100 scale (grids/A): 2.294965 object centre (A): 5.139500 6.641500 -3.453501 number of atom coordinates read : 5346 total number of charged atoms : 5190 net assigned charge : 10.00004 assigned positive charge : 843.9109 centred at (gu) : 89.61997 90.00119 89.95528 assigned negative charge : -833.9188 centred at (gu) : 89.58965 89.78307 90.06812 start vw surface at 0.2200000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 236990 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44317 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 108470 mr = 176410 m= 27449 mr = 86365 m= 3745 mr = 20121 m= 145 mr = 2339 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 7120 time to turn everything in is 1.790000 number of dielectric boundary points 91540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 41412 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) : 1.529976 object centre at (A) : 5.139500 6.641500 -3.453501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1321084 -2.6406648E-02 midg,1,midg; midg,igrid,midg -0.3475603 0.2163771 1,midg,midg; igrid,midg,midg -0.2872362 0.6422172 gauss-seidel spectral radius is 0.9991831 estimated iterations to convergence 276 setup time was (sec) 2.140000 now iterating at: 11:03:13 rms-change max change #iterations 11.13601 345.7826 at 10iterations 6.446104 176.2909 at 20iterations 3.695601 86.55235 at 30iterations 2.105655 44.83154 at 40iterations 1.198602 27.13313 at 50iterations 0.6761250 11.93828 at 60iterations 0.3823592 8.184406 at 70iterations 0.2156232 4.161842 at 80iterations 0.1209214 2.515761 at 90iterations 6.8108618E-02 1.273928 at 100iterations 3.8295161E-02 0.7211223 at 110iterations 2.1501465E-02 0.3948498 at 120iterations 1.2086998E-02 0.2443454 at 130iterations 6.8198661E-03 0.1354861 at 140iterations 3.8813518E-03 7.8083038E-02 at 150iterations 2.2497780E-03 4.9543381E-02 at 160iterations 1.3606152E-03 2.8713226E-02 at 170iterations 8.7800523E-04 1.8538475E-02 at 180iterations finished qdiffx linear iterations at : 11:03:25 total time elapsed so far: 13.59000 # loops : 180 mean,max change (kT/e) : 8.7800523E-04 1.8538475E-02 energy calculations done at 13.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.76000 DelPhi exited at 11:03:25 13.760u 0.252s 0:14.32 97.8% 0+0k 0+0io 0pf+0w