Sun Oct 9 13:56:52 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 13:56:52 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7060130 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): -1.181000 45.50400 ymin,ymax (A): 36.28300 86.70700 zmin,zma (A): -24.66200 25.11000 x,y,z range (A): 46.68500 50.42400 49.77200 scale (grids/A): 0.7060130 object centre (A): 22.16150 61.49500 0.2240000 number of atom coordinates read : 2371 total number of charged atoms : 2230 net assigned charge : 3.500021 assigned positive charge : 365.0092 centred at (gu) : 90.00102 90.02616 91.63136 assigned negative charge : -361.5095 centred at (gu) : 90.13557 90.11916 91.55858 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 8084 nv = 96 ne = 84 npr = 47773 no. pairs analyzed = 47773 no. exposed pairs = 3008 no. arc points = 21166 no. surface atoms = 997 nbur = 1374 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 509 mr = 4468 m= 4 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.1800000 number of dielectric boundary points 4053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1916 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8906 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.8249834E-09 9.3600903E-08 midg,1,midg; midg,igrid,midg 7.8473938E-08 -2.4264532E-08 1,midg,midg; igrid,midg,midg 1.0134612E-07 -4.7678640E-08 gauss-seidel spectral radius is 0.9895757 estimated iterations to convergence 80 setup time was (sec) 0.4000000 now iterating at: 13:56:52 rms-change max change #iterations 0.2171444 26.17181 at 10iterations 2.7023166E-02 3.943657 at 20iterations 3.9991848E-03 0.5511932 at 30iterations 8.8559440E-04 0.1356163 at 40iterations 2.7798800E-04 4.1435242E-02 at 50iterations finished qdiffx linear iterations at : 13:56:56 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 2.7798800E-04 4.1435242E-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) 3.680000 DelPhi exited at 13:56:56 3.685u 0.228s 0:04.21 92.6% 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 13:56:56 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.118039 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): -1.181000 45.50400 ymin,ymax (A): 36.28300 86.70700 zmin,zma (A): -24.66200 25.11000 x,y,z range (A): 46.68500 50.42400 49.77200 scale (grids/A): 2.118039 object centre (A): 22.16150 61.49500 0.2240000 number of atom coordinates read : 2371 total number of charged atoms : 2230 net assigned charge : 3.500021 assigned positive charge : 365.0092 centred at (gu) : 90.00275 90.07813 94.89384 assigned negative charge : -361.5095 centred at (gu) : 90.40643 90.35716 94.67558 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85727 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21166 grid for indexing accessible points = 1.400000 m= 33341 mr = 59601 m= 6075 mr = 24947 m= 537 mr = 3839 m= 19 mr = 275 m= 0 mr = 8 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 154 time to turn everything in is 0.4300000 number of dielectric boundary points 37029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 17679 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) : 0.7060130 object centre at (A) : 22.16150 61.49500 0.2240000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4421336E-02 3.1286862E-02 midg,1,midg; midg,igrid,midg 0.1091388 3.3220300E-03 1,midg,midg; igrid,midg,midg -5.4490743E-03 -1.6765689E-02 gauss-seidel spectral radius is 0.9988657 estimated iterations to convergence 235 setup time was (sec) 0.6700000 now iterating at: 13:56:57 rms-change max change #iterations 5.054670 272.4581 at 10iterations 2.523609 85.56409 at 20iterations 1.259493 35.41471 at 30iterations 0.6334695 19.38813 at 40iterations 0.3171310 10.31661 at 50iterations 0.1593669 4.690384 at 60iterations 8.0356717E-02 2.320496 at 70iterations 4.0144578E-02 1.118941 at 80iterations 2.0358780E-02 0.5930099 at 90iterations 1.0425193E-02 0.3198280 at 100iterations 5.3911586E-03 0.1702881 at 110iterations 2.8906355E-03 8.5725784E-02 at 120iterations finished qdiffx linear iterations at : 13:57:05 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 2.8906355E-03 8.5725784E-02 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.390000 DelPhi exited at 13:57:05 8.391u 0.235s 0:08.98 95.9% 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 13:57:05 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.177058 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): -1.181000 45.50400 ymin,ymax (A): 36.28300 86.70700 zmin,zma (A): -24.66200 25.11000 x,y,z range (A): 46.68500 50.42400 49.77200 scale (grids/A): 3.177058 object centre (A): 22.16150 61.49500 0.2240000 number of atom coordinates read : 2371 total number of charged atoms : 2230 net assigned charge : 3.500021 assigned positive charge : 365.0092 centred at (gu) : 90.00380 90.11702 97.34070 assigned negative charge : -361.5095 centred at (gu) : 90.60959 90.53571 97.01327 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 197545 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21166 grid for indexing accessible points = 1.400000 m= 104775 mr = 143891 m= 41037 mr = 86350 m= 11176 mr = 33166 m= 2167 mr = 8490 m= 262 mr = 1561 m= 13 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 482 time to turn everything in is 1.360000 number of dielectric boundary points 83354 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 17840 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) : 2.118039 object centre at (A) : 22.16150 61.49500 0.2240000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2567158 0.4669928 midg,1,midg; midg,igrid,midg 1.593281 -0.1005431 1,midg,midg; igrid,midg,midg -0.1097794 -0.1246051 gauss-seidel spectral radius is 0.9993114 estimated iterations to convergence 301 setup time was (sec) 1.630000 now iterating at: 13:57:07 rms-change max change #iterations 11.28421 450.2801 at 10iterations 6.708395 168.7387 at 20iterations 3.982004 86.45384 at 30iterations 2.365885 49.79707 at 40iterations 1.400235 27.10996 at 50iterations 0.8275658 15.36504 at 60iterations 0.4876778 8.937889 at 70iterations 0.2878688 5.213027 at 80iterations 0.1699717 2.986164 at 90iterations 0.1002713 1.801236 at 100iterations 5.9256695E-02 0.9772491 at 110iterations 3.5249334E-02 0.7066564 at 120iterations 2.1133235E-02 0.3769379 at 130iterations 1.2911737E-02 0.2252502 at 140iterations 8.1668617E-03 0.1590166 at 150iterations 5.3953510E-03 0.1090012 at 160iterations 3.7982995E-03 8.1260681E-02 at 170iterations 2.8451623E-03 5.6369781E-02 at 180iterations finished qdiffx linear iterations at : 13:57:20 total time elapsed so far: 14.55000 # loops : 180 mean,max change (kT/e) : 2.8451623E-03 5.6369781E-02 energy calculations done at 14.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.69000 DelPhi exited at 13:57:20 14.692u 0.249s 0:15.23 98.0% 0+0k 0+0io 0pf+0w