Sat Oct 8 16:24:02 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 8 2011 at 16:24:02 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 = 2426 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: 0.6597235 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): -18.23200 30.32400 ymin,ymax (A): 3.827000 50.20700 zmin,zma (A): -17.07800 36.88400 x,y,z range (A): 48.55600 46.38000 53.96200 scale (grids/A): 0.6597235 object centre (A): 6.046000 27.01700 9.902999 number of atom coordinates read : 2426 total number of charged atoms : 2367 net assigned charge : 2.000003 assigned positive charge : 365.6509 centred at (gu) : 88.98350 90.98306 90.48577 assigned negative charge : -363.6517 centred at (gu) : 88.94841 90.80216 90.58923 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7226 nv = 96 ne = 84 npr = 48001 no. pairs analyzed = 48001 no. exposed pairs = 3135 no. arc points = 21270 no. surface atoms = 1071 nbur = 1355 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 4020 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2104 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8639 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1403512E-08 -1.5927455E-08 midg,1,midg; midg,igrid,midg -2.3506464E-08 4.6189371E-08 1,midg,midg; igrid,midg,midg -2.0412401E-09 9.1772145E-09 gauss-seidel spectral radius is 0.9880794 estimated iterations to convergence 75 setup time was (sec) 0.5300000 now iterating at: 16:24:03 rms-change max change #iterations 0.1598029 26.14231 at 10iterations 1.6787816E-02 2.204538 at 20iterations 1.8873712E-03 0.2468640 at 30iterations 2.8687093E-04 3.6957741E-02 at 40iterations 7.2744602E-05 1.0015965E-02 at 50iterations finished qdiffx linear iterations at : 16:24:06 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 7.2744602E-05 1.0015965E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 16:24:06 3.323u 0.186s 0:03.81 91.8% 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 16:24:06 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 = 2426 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.979171 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): -18.23200 30.32400 ymin,ymax (A): 3.827000 50.20700 zmin,zma (A): -17.07800 36.88400 x,y,z range (A): 48.55600 46.38000 53.96200 scale (grids/A): 1.979171 object centre (A): 6.046000 27.01700 9.902999 number of atom coordinates read : 2426 total number of charged atoms : 2367 net assigned charge : 2.000003 assigned positive charge : 365.6509 centred at (gu) : 86.95018 92.94851 91.45693 assigned negative charge : -363.6517 centred at (gu) : 86.84491 92.40615 91.76756 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21270 grid for indexing accessible points = 1.400000 m= 29020 mr = 54286 m= 5554 mr = 21584 m= 450 mr = 3834 m= 9 mr = 226 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 222 time to turn everything in is 0.5500000 number of dielectric boundary points 32781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18688 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) : 0.6597235 object centre at (A) : 6.046000 27.01700 9.902999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5871493E-02 -1.9165616E-02 midg,1,midg; midg,igrid,midg -8.9352736E-03 2.6575835E-02 1,midg,midg; igrid,midg,midg -3.9072130E-02 4.4119875E-03 gauss-seidel spectral radius is 0.9987191 estimated iterations to convergence 221 setup time was (sec) 0.8200000 now iterating at: 16:24:07 rms-change max change #iterations 4.444220 218.5462 at 10iterations 2.127267 75.93154 at 20iterations 1.019044 32.51625 at 30iterations 0.4900043 16.91443 at 40iterations 0.2363480 7.602288 at 50iterations 0.1130312 3.504012 at 60iterations 5.4447640E-02 1.678175 at 70iterations 2.6141554E-02 0.7821140 at 80iterations 1.2598825E-02 0.3694839 at 90iterations 6.0666227E-03 0.1977596 at 100iterations 2.9276758E-03 8.7098122E-02 at 110iterations 1.4177855E-03 4.1654587E-02 at 120iterations finished qdiffx linear iterations at : 16:24:13 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 1.4177855E-03 4.1654587E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 16:24:14 7.008u 0.169s 0:07.47 95.8% 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 16:24:14 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 = 2426 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: 2.968756 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): -18.23200 30.32400 ymin,ymax (A): 3.827000 50.20700 zmin,zma (A): -17.07800 36.88400 x,y,z range (A): 48.55600 46.38000 53.96200 scale (grids/A): 2.968756 object centre (A): 6.046000 27.01700 9.902999 number of atom coordinates read : 2426 total number of charged atoms : 2367 net assigned charge : 2.000003 assigned positive charge : 365.6509 centred at (gu) : 85.42511 94.42262 92.18525 assigned negative charge : -363.6517 centred at (gu) : 85.26736 93.60914 92.65130 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 179692 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21270 grid for indexing accessible points = 1.400000 m= 91342 mr = 131413 m= 35886 mr = 74909 m= 10526 mr = 29441 m= 2063 mr = 8286 m= 207 mr = 1598 m= 7 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 631 time to turn everything in is 1.380000 number of dielectric boundary points 73953 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 18936 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) : 1.979171 object centre at (A) : 6.046000 27.01700 9.902999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2237990 -0.2442315 midg,1,midg; midg,igrid,midg -0.1011164 0.1772635 1,midg,midg; igrid,midg,midg -0.5228974 7.1401000E-02 gauss-seidel spectral radius is 0.9992834 estimated iterations to convergence 295 setup time was (sec) 1.660000 now iterating at: 16:24:15 rms-change max change #iterations 10.35667 409.1252 at 10iterations 6.128889 156.3344 at 20iterations 3.617760 82.08491 at 30iterations 2.129170 44.13060 at 40iterations 1.247064 23.66866 at 50iterations 0.7309251 15.01044 at 60iterations 0.4272583 7.657185 at 70iterations 0.2491327 4.459939 at 80iterations 0.1452765 2.419845 at 90iterations 8.4599800E-02 1.572065 at 100iterations 4.9352184E-02 0.8481178 at 110iterations 2.8654192E-02 0.4745979 at 120iterations 1.6648786E-02 0.2865257 at 130iterations 9.6869227E-03 0.1615944 at 140iterations 5.6324704E-03 0.1013184 at 150iterations 3.2733683E-03 5.5260181E-02 at 160iterations 1.9046322E-03 3.1241417E-02 at 170iterations 1.1136583E-03 2.2262573E-02 at 180iterations finished qdiffx linear iterations at : 16:24:25 total time elapsed so far: 11.15000 # loops : 180 mean,max change (kT/e) : 1.1136583E-03 2.2262573E-02 energy calculations done at 11.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.32000 DelPhi exited at 16:24:26 11.323u 0.188s 0:11.96 96.1% 0+0k 0+0io 0pf+0w