Sat Oct 8 18:27:12 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 18:27:12 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3325 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5568068 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): -19.80900 39.90300 ymin,ymax (A): -2.182000 53.69200 zmin,zma (A): 5.287000 69.22300 x,y,z range (A): 59.71200 55.87400 63.93600 scale (grids/A): 0.5568068 object centre (A): 10.04700 25.75500 37.25500 number of atom coordinates read : 3325 total number of charged atoms : 3181 net assigned charge : 6.500046 assigned positive charge : 500.4985 centred at (gu) : 89.66039 90.89790 90.21787 assigned negative charge : -493.9998 centred at (gu) : 89.82440 90.94210 90.22913 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7036 nv = 96 ne = 84 npr = 64896 no. pairs analyzed = 64896 no. exposed pairs = 4557 no. arc points = 33174 no. surface atoms = 1504 nbur = 1821 mkacc time = 0.1900000 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 = 1.568000 m= 339 mr = 3480 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3292 ## 404 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8937 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9946821E-10 5.1473037E-10 midg,1,midg; midg,igrid,midg 8.8373531E-10 1.4825406E-10 1,midg,midg; igrid,midg,midg 2.5841076E-09 -1.1240068E-09 gauss-seidel spectral radius is 0.9834055 estimated iterations to convergence 64 setup time was (sec) 0.6800000 now iterating at: 18:27:13 rms-change max change #iterations 8.3204173E-02 14.03640 at 10iterations 6.2982300E-03 0.8784866 at 20iterations 6.9351599E-04 0.1002045 at 30iterations 1.4182743E-04 2.0656586E-02 at 40iterations 3.4993227E-05 5.1841736E-03 at 50iterations finished qdiffx linear iterations at : 18:27:16 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 3.4993227E-05 5.1841736E-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) 4.130000 DelPhi exited at 18:27:17 4.138u 0.264s 0:04.67 94.0% 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 18:27:17 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3325 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.670420 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): -19.80900 39.90300 ymin,ymax (A): -2.182000 53.69200 zmin,zma (A): 5.287000 69.22300 x,y,z range (A): 59.71200 55.87400 63.93600 scale (grids/A): 1.670420 object centre (A): 10.04700 25.75500 37.25500 number of atom coordinates read : 3325 total number of charged atoms : 3181 net assigned charge : 6.500046 assigned positive charge : 500.4985 centred at (gu) : 88.98015 92.69262 90.65252 assigned negative charge : -493.9998 centred at (gu) : 89.47305 92.82610 90.68669 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 76834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33174 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24510 mr = 50590 m= 2860 mr = 16388 m= 98 mr = 1400 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 706 time to turn everything in is 0.6900000 number of dielectric boundary points 35915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 376 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 24440 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) : 0.5568068 object centre at (A) : 10.04700 25.75500 37.25500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1063324E-03 -4.4603017E-03 midg,1,midg; midg,igrid,midg 2.5791882E-03 5.3816329E-04 1,midg,midg; igrid,midg,midg 1.6333651E-02 -1.1916811E-02 gauss-seidel spectral radius is 0.9983258 estimated iterations to convergence 194 setup time was (sec) 0.9800000 now iterating at: 18:27:18 rms-change max change #iterations 3.761366 215.5644 at 10iterations 1.611869 55.49780 at 20iterations 0.6929618 24.20810 at 30iterations 0.2991838 11.04352 at 40iterations 0.1298166 4.188337 at 50iterations 5.5787485E-02 1.896814 at 60iterations 2.4087613E-02 0.8690128 at 70iterations 1.0404130E-02 0.3402672 at 80iterations 4.5237863E-03 0.1463070 at 90iterations 1.9651884E-03 6.2339783E-02 at 100iterations 8.6122873E-04 2.7435303E-02 at 110iterations 3.8492904E-04 1.2649536E-02 at 120iterations finished qdiffx linear iterations at : 18:27:26 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 3.8492904E-04 1.2649536E-02 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.470000 DelPhi exited at 18:27:27 9.475u 0.304s 0:10.04 97.3% 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 18:27:27 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3325 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.505630 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): -19.80900 39.90300 ymin,ymax (A): -2.182000 53.69200 zmin,zma (A): 5.287000 69.22300 x,y,z range (A): 59.71200 55.87400 63.93600 scale (grids/A): 2.505630 object centre (A): 10.04700 25.75500 37.25500 number of atom coordinates read : 3325 total number of charged atoms : 3181 net assigned charge : 6.500046 assigned positive charge : 500.4985 centred at (gu) : 88.46998 94.03853 90.97850 assigned negative charge : -493.9998 centred at (gu) : 89.20956 94.23900 91.03003 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 178196 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33174 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 82699 mr = 124030 m= 25167 mr = 64092 m= 4556 mr = 18676 m= 353 mr = 2898 m= 7 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 2445 time to turn everything in is 1.690000 number of dielectric boundary points 81161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 25427 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) : 1.670420 object centre at (A) : 10.04700 25.75500 37.25500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1117316 -0.2368907 midg,1,midg; midg,igrid,midg -2.5105944E-02 9.7837985E-02 1,midg,midg; igrid,midg,midg 0.1846404 -0.1711664 gauss-seidel spectral radius is 0.9991974 estimated iterations to convergence 279 setup time was (sec) 2.030000 now iterating at: 18:27:29 rms-change max change #iterations 9.686525 371.0417 at 10iterations 5.650177 137.2700 at 20iterations 3.262719 74.02959 at 30iterations 1.868112 41.96873 at 40iterations 1.066851 23.69478 at 50iterations 0.6071897 14.26334 at 60iterations 0.3437479 7.493241 at 70iterations 0.1952126 4.256498 at 80iterations 0.1100542 2.164628 at 90iterations 6.2269311E-02 1.363357 at 100iterations 3.5091847E-02 0.7573805 at 110iterations 1.9781416E-02 0.4453072 at 120iterations 1.1136006E-02 0.2800369 at 130iterations 6.2864376E-03 0.1206703 at 140iterations 3.5286858E-03 6.8893433E-02 at 150iterations 1.9829418E-03 4.3416977E-02 at 160iterations 1.1154709E-03 2.2409439E-02 at 170iterations 6.2838243E-04 1.2538910E-02 at 180iterations finished qdiffx linear iterations at : 18:27:43 total time elapsed so far: 15.81000 # loops : 180 mean,max change (kT/e) : 6.2838243E-04 1.2538910E-02 energy calculations done at 15.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.98000 DelPhi exited at 18:27:43 15.986u 0.325s 0:16.59 98.2% 0+0k 0+0io 0pf+0w