Sat Oct 15 14:46:09 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 Sat Oct 15 2011 at 14:46:09 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 = 2738 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5697276 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): -13.64900 48.83700 ymin,ymax (A): -27.22000 17.85600 zmin,zma (A): -41.71800 5.655000 x,y,z range (A): 62.48600 45.07600 47.37300 scale (grids/A): 0.5697276 object centre (A): 17.59400 -4.682000 -18.03150 number of atom coordinates read : 2738 total number of charged atoms : 2599 net assigned charge : -1.499974 assigned positive charge : 410.0164 centred at (gu) : 89.93684 89.79457 89.06767 assigned negative charge : -411.5174 centred at (gu) : 89.97456 89.62513 88.89545 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5863 nv = 96 ne = 84 npr = 54117 no. pairs analyzed = 54117 no. exposed pairs = 3655 no. arc points = 26121 no. surface atoms = 1228 nbur = 1510 mkacc time = 0.1500000 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= 229 mr = 2917 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2642 ## 327 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7521 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4167718E-09 1.7852231E-09 midg,1,midg; midg,igrid,midg -2.8189002E-09 2.0913808E-09 1,midg,midg; igrid,midg,midg 3.5422290E-10 -7.2627260E-10 gauss-seidel spectral radius is 0.9840890 estimated iterations to convergence 65 setup time was (sec) 0.6300000 now iterating at: 14:46:10 rms-change max change #iterations 8.3765484E-02 12.32751 at 10iterations 6.2648272E-03 1.168740 at 20iterations 4.6923739E-04 7.3524475E-02 at 30iterations 3.4712739E-05 6.6061020E-03 at 40iterations 2.6945477E-06 4.3749809E-04 at 50iterations finished qdiffx linear iterations at : 14:46:14 total time elapsed so far: 5.190000 # loops : 50 mean,max change (kT/e) : 2.6945477E-06 4.3749809E-04 energy calculations done at 5.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.370000 DelPhi exited at 14:46:15 5.373u 0.446s 0:06.10 95.2% 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 15 2011 at 14:46:15 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 = 2738 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.709183 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): -13.64900 48.83700 ymin,ymax (A): -27.22000 17.85600 zmin,zma (A): -41.71800 5.655000 x,y,z range (A): 62.48600 45.07600 47.37300 scale (grids/A): 1.709183 object centre (A): 17.59400 -4.682000 -18.03150 number of atom coordinates read : 2738 total number of charged atoms : 2599 net assigned charge : -1.499974 assigned positive charge : 410.0164 centred at (gu) : 89.80982 89.38320 87.20245 assigned negative charge : -411.5174 centred at (gu) : 89.92334 88.87527 86.68607 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 64600 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26121 grid for indexing accessible points = 1.400000 m= 19337 mr = 42630 m= 2008 mr = 13054 m= 55 mr = 944 m= 0 mr = 9 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 469 time to turn everything in is 0.5400000 number of dielectric boundary points 29363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 279 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 20127 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) : 0.5697276 object centre at (A) : 17.59400 -4.682000 -18.03150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1246420E-02 5.3423429E-03 midg,1,midg; midg,igrid,midg -6.4002159E-03 5.1302486E-03 1,midg,midg; igrid,midg,midg 1.0943947E-02 6.6405773E-04 gauss-seidel spectral radius is 0.9983280 estimated iterations to convergence 194 setup time was (sec) 0.8800000 now iterating at: 14:46:16 rms-change max change #iterations 3.486453 167.3396 at 10iterations 1.508961 59.52479 at 20iterations 0.6512194 23.53610 at 30iterations 0.2821162 10.35941 at 40iterations 0.1219902 4.766758 at 50iterations 5.2575324E-02 2.057866 at 60iterations 2.2658080E-02 0.7950611 at 70iterations 9.8135741E-03 0.3694210 at 80iterations 4.2465259E-03 0.1505163 at 90iterations 1.8314801E-03 7.6660156E-02 at 100iterations 7.9430209E-04 2.8632104E-02 at 110iterations 3.4176873E-04 1.1858940E-02 at 120iterations finished qdiffx linear iterations at : 14:46:28 total time elapsed so far: 12.85000 # loops : 120 mean,max change (kT/e) : 3.4176873E-04 1.1858940E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 14:46:29 13.042u 0.517s 0:13.87 97.6% 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 Sat Oct 15 2011 at 14:46:29 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 = 2738 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.563774 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): -13.64900 48.83700 ymin,ymax (A): -27.22000 17.85600 zmin,zma (A): -41.71800 5.655000 x,y,z range (A): 62.48600 45.07600 47.37300 scale (grids/A): 2.563774 object centre (A): 17.59400 -4.682000 -18.03150 number of atom coordinates read : 2738 total number of charged atoms : 2599 net assigned charge : -1.499974 assigned positive charge : 410.0164 centred at (gu) : 89.71439 89.07444 85.80354 assigned negative charge : -411.5174 centred at (gu) : 89.88493 88.31271 85.02907 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 150015 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26121 grid for indexing accessible points = 1.400000 m= 67313 mr = 104779 m= 18784 mr = 52405 m= 2985 mr = 13800 m= 178 mr = 1880 m= 3 mr = 95 m= 0 mr = 2 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 1502 time to turn everything in is 1.350000 number of dielectric boundary points 66317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 20783 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) : 1.709183 object centre at (A) : 17.59400 -4.682000 -18.03150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2642285 9.1464959E-02 midg,1,midg; midg,igrid,midg -6.7578532E-02 5.2789938E-02 1,midg,midg; igrid,midg,midg 0.1842525 0.3573991 gauss-seidel spectral radius is 0.9991855 estimated iterations to convergence 277 setup time was (sec) 1.740000 now iterating at: 14:46:31 rms-change max change #iterations 8.932621 339.2862 at 10iterations 5.117773 140.1312 at 20iterations 2.922503 78.26686 at 30iterations 1.653644 39.66634 at 40iterations 0.9345914 20.79991 at 50iterations 0.5258480 10.81802 at 60iterations 0.2957128 6.214859 at 70iterations 0.1658810 3.444426 at 80iterations 9.2837438E-02 2.080139 at 90iterations 5.2183401E-02 1.100130 at 100iterations 2.9176246E-02 0.5817490 at 110iterations 1.6305307E-02 0.3397312 at 120iterations 9.1342563E-03 0.1844788 at 130iterations 5.1048370E-03 0.1042963 at 140iterations 2.8487148E-03 5.7496071E-02 at 150iterations 1.5945906E-03 3.4404755E-02 at 160iterations 8.8932301E-04 1.7843246E-02 at 170iterations 4.9711548E-04 1.0089874E-02 at 180iterations finished qdiffx linear iterations at : 14:46:52 total time elapsed so far: 22.54000 # loops : 180 mean,max change (kT/e) : 4.9711548E-04 1.0089874E-02 energy calculations done at 22.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.71000 DelPhi exited at 14:46:52 22.719u 0.520s 0:23.52 98.7% 0+0k 0+0io 0pf+0w