Tue Oct 11 08:32:21 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 Tue Oct 11 2011 at 08:32:21 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 = 2116 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7187853 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): -8.488000 38.40700 ymin,ymax (A): -30.12200 19.40600 zmin,zma (A): 3.758000 46.38800 x,y,z range (A): 46.89500 49.52800 42.63000 scale (grids/A): 0.7187853 object centre (A): 14.95950 -5.358000 25.07300 number of atom coordinates read : 2116 total number of charged atoms : 1988 net assigned charge : 6.500009 assigned positive charge : 322.7539 centred at (gu) : 90.55817 89.16787 90.29509 assigned negative charge : -316.2541 centred at (gu) : 90.43487 89.21317 90.39850 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7479 nv = 96 ne = 84 npr = 42319 no. pairs analyzed = 42319 no. exposed pairs = 2522 no. arc points = 17244 no. surface atoms = 864 nbur = 1252 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 508 mr = 4403 m= 1 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1541 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8141 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2922986E-07 3.7230694E-09 midg,1,midg; midg,igrid,midg 1.1695467E-07 3.5993054E-08 1,midg,midg; igrid,midg,midg -7.9092493E-09 1.6606836E-07 gauss-seidel spectral radius is 0.9899108 estimated iterations to convergence 81 setup time was (sec) 0.3600000 now iterating at: 08:32:22 rms-change max change #iterations 0.2117589 39.53348 at 10iterations 2.7694913E-02 3.702701 at 20iterations 3.6257524E-03 0.4601212 at 30iterations 5.5933982E-04 7.6267242E-02 at 40iterations 1.2922140E-04 1.5933990E-02 at 50iterations finished qdiffx linear iterations at : 08:32:25 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.2922140E-04 1.5933990E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 08:32:25 3.386u 0.171s 0:03.86 91.9% 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 Tue Oct 11 2011 at 08:32:25 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 = 2116 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: 2.156356 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): -8.488000 38.40700 ymin,ymax (A): -30.12200 19.40600 zmin,zma (A): 3.758000 46.38800 x,y,z range (A): 46.89500 49.52800 42.63000 scale (grids/A): 2.156356 object centre (A): 14.95950 -5.358000 25.07300 number of atom coordinates read : 2116 total number of charged atoms : 1988 net assigned charge : 6.500009 assigned positive charge : 322.7539 centred at (gu) : 91.67457 87.50361 90.88497 assigned negative charge : -316.2541 centred at (gu) : 91.30494 87.63957 91.19572 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 79287 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17244 grid for indexing accessible points = 1.400000 m= 32847 mr = 57043 m= 6450 mr = 25302 m= 547 mr = 4326 m= 16 mr = 279 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 32197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15806 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) : 0.7187853 object centre at (A) : 14.95950 -5.358000 25.07300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6377959E-02 2.4031876E-02 midg,1,midg; midg,igrid,midg 4.4431940E-02 3.8102113E-02 1,midg,midg; igrid,midg,midg -4.3267015E-02 3.5450932E-02 gauss-seidel spectral radius is 0.9988656 estimated iterations to convergence 235 setup time was (sec) 0.6100000 now iterating at: 08:32:26 rms-change max change #iterations 4.776394 196.3947 at 10iterations 2.376946 86.16786 at 20iterations 1.197067 37.06387 at 30iterations 0.6003320 17.97350 at 40iterations 0.3013214 8.971052 at 50iterations 0.1509107 4.213371 at 60iterations 7.5884089E-02 2.211599 at 70iterations 3.8156740E-02 1.116954 at 80iterations 1.9241443E-02 0.6318893 at 90iterations 9.7323954E-03 0.3161855 at 100iterations 4.9625579E-03 0.1640854 at 110iterations 2.5660184E-03 7.2123051E-02 at 120iterations finished qdiffx linear iterations at : 08:32:33 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 2.5660184E-03 7.2123051E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 08:32:34 7.870u 0.228s 0:08.43 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 Tue Oct 11 2011 at 08:32:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2116 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: 3.234534 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): -8.488000 38.40700 ymin,ymax (A): -30.12200 19.40600 zmin,zma (A): 3.758000 46.38800 x,y,z range (A): 46.89500 49.52800 42.63000 scale (grids/A): 3.234534 object centre (A): 14.95950 -5.358000 25.07300 number of atom coordinates read : 2116 total number of charged atoms : 1988 net assigned charge : 6.500009 assigned positive charge : 322.7539 centred at (gu) : 92.51180 86.25546 91.32747 assigned negative charge : -316.2541 centred at (gu) : 91.95733 86.45936 91.79356 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 182728 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17244 grid for indexing accessible points = 1.400000 m= 101682 mr = 137054 m= 42509 mr = 85397 m= 12188 mr = 35265 m= 2325 mr = 9595 m= 286 mr = 1640 m= 8 mr = 171 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 72604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 15904 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) : 2.156356 object centre at (A) : 14.95950 -5.358000 25.07300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1303322 0.1920266 midg,1,midg; midg,igrid,midg 0.3067388 0.2474339 1,midg,midg; igrid,midg,midg -0.4716431 0.2949430 gauss-seidel spectral radius is 0.9993056 estimated iterations to convergence 299 setup time was (sec) 1.490000 now iterating at: 08:32:35 rms-change max change #iterations 10.60789 455.6619 at 10iterations 6.288341 151.9156 at 20iterations 3.736982 78.72520 at 30iterations 2.218698 46.01783 at 40iterations 1.311905 25.48871 at 50iterations 0.7735526 13.18549 at 60iterations 0.4568659 7.567944 at 70iterations 0.2690910 5.170492 at 80iterations 0.1584362 2.761070 at 90iterations 9.3444996E-02 1.520775 at 100iterations 5.4984115E-02 0.9347401 at 110iterations 3.2556210E-02 0.5735245 at 120iterations 1.9347176E-02 0.3510590 at 130iterations 1.1634352E-02 0.2238274 at 140iterations 7.1465070E-03 0.1264954 at 150iterations 4.5264838E-03 8.2078934E-02 at 160iterations 3.0092765E-03 5.3997040E-02 at 170iterations 2.1249193E-03 4.1461945E-02 at 180iterations finished qdiffx linear iterations at : 08:32:47 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 2.1249193E-03 4.1461945E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 08:32:47 12.933u 0.189s 0:13.62 96.2% 0+0k 0+0io 0pf+0w