Sat Oct 15 12:02:17 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 12:02:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3313 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5554342 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): -49.90300 5.155000 ymin,ymax (A): 185.8230 247.0290 zmin,zma (A): 69.42800 133.5220 x,y,z range (A): 55.05800 61.20601 64.09400 scale (grids/A): 0.5554342 object centre (A): -22.37400 216.4260 101.4750 number of atom coordinates read : 3313 total number of charged atoms : 3171 net assigned charge : 12.00004 assigned positive charge : 486.2036 centred at (gu) : 90.15962 89.35537 90.38390 assigned negative charge : -474.2054 centred at (gu) : 90.06460 89.26331 90.50768 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6942 nv = 96 ne = 84 npr = 63781 no. pairs analyzed = 63781 no. exposed pairs = 4631 no. arc points = 32946 no. surface atoms = 1527 nbur = 1786 mkacc time = 0.2100000 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= 317 mr = 3401 m= 0 mr = 14 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.4800000 number of dielectric boundary points 3844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3301 ## 405 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 8906 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1054962E-09 -1.9681605E-10 midg,1,midg; midg,igrid,midg 1.6984711E-10 1.7130329E-09 1,midg,midg; igrid,midg,midg 1.1966372E-10 2.1095230E-09 gauss-seidel spectral radius is 0.9833251 estimated iterations to convergence 64 setup time was (sec) 0.8400000 now iterating at: 12:02:18 rms-change max change #iterations 8.1700973E-02 13.97683 at 10iterations 5.7533216E-03 0.8060436 at 20iterations 4.0890713E-04 5.8805943E-02 at 30iterations 3.3477016E-05 4.6136379E-03 at 40iterations 4.2035072E-06 4.5204163E-04 at 50iterations finished qdiffx linear iterations at : 12:02:22 total time elapsed so far: 4.900000 # loops : 50 mean,max change (kT/e) : 4.2035072E-06 4.5204163E-04 energy calculations done at 4.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.120000 DelPhi exited at 12:02:23 5.121u 0.443s 0:05.92 93.9% 0+0k 0+0io 6pf+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 12:02:23 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 = 3313 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.666303 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): -49.90300 5.155000 ymin,ymax (A): 185.8230 247.0290 zmin,zma (A): 69.42800 133.5220 x,y,z range (A): 55.05800 61.20601 64.09400 scale (grids/A): 1.666303 object centre (A): -22.37400 216.4260 101.4750 number of atom coordinates read : 3313 total number of charged atoms : 3171 net assigned charge : 12.00004 assigned positive charge : 486.2036 centred at (gu) : 90.47806 88.06515 91.15076 assigned negative charge : -474.2054 centred at (gu) : 90.19328 87.78961 91.52261 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 76291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32946 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24144 mr = 49972 m= 2799 mr = 16048 m= 77 mr = 1353 m= 0 mr = 13 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 473 time to turn everything in is 0.8100000 number of dielectric boundary points 35925 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 333 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 24378 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) : 0.5554342 object centre at (A) : -22.37400 216.4260 101.4750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9894362E-03 -7.2935922E-03 midg,1,midg; midg,igrid,midg -3.8252925E-03 2.4074109E-02 1,midg,midg; igrid,midg,midg 7.1744910E-03 1.6284421E-02 gauss-seidel spectral radius is 0.9983170 estimated iterations to convergence 194 setup time was (sec) 1.170000 now iterating at: 12:02:24 rms-change max change #iterations 3.606239 206.2725 at 10iterations 1.541470 76.47726 at 20iterations 0.6602373 20.77920 at 30iterations 0.2839419 9.888885 at 40iterations 0.1217940 4.038712 at 50iterations 5.2528966E-02 1.868835 at 60iterations 2.2567876E-02 0.7565231 at 70iterations 9.6931532E-03 0.3345108 at 80iterations 4.1716220E-03 0.1389790 at 90iterations 1.7931436E-03 6.1325550E-02 at 100iterations 7.7280682E-04 2.4174690E-02 at 110iterations 3.3342838E-04 1.2376785E-02 at 120iterations finished qdiffx linear iterations at : 12:02:35 total time elapsed so far: 12.31000 # loops : 120 mean,max change (kT/e) : 3.3342838E-04 1.2376785E-02 energy calculations done at 12.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 12:02:36 12.540u 0.482s 0:13.40 97.1% 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 12:02:36 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 = 3313 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.499454 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): -49.90300 5.155000 ymin,ymax (A): 185.8230 247.0290 zmin,zma (A): 69.42800 133.5220 x,y,z range (A): 55.05800 61.20601 64.09400 scale (grids/A): 2.499454 object centre (A): -22.37400 216.4260 101.4750 number of atom coordinates read : 3313 total number of charged atoms : 3171 net assigned charge : 12.00004 assigned positive charge : 486.2036 centred at (gu) : 90.71680 87.09734 91.72591 assigned negative charge : -474.2054 centred at (gu) : 90.28997 86.68433 92.28387 start vw surface at 0.1700000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 176871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32946 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 81791 mr = 123071 m= 24605 mr = 62850 m= 4437 mr = 18023 m= 357 mr = 2860 m= 3 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 1655 time to turn everything in is 1.970000 number of dielectric boundary points 81094 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 25347 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) : 1.666303 object centre at (A) : -22.37400 216.4260 101.4750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1149463 -4.4687953E-02 midg,1,midg; midg,igrid,midg -0.1870160 0.3677638 1,midg,midg; igrid,midg,midg 0.1274736 0.1756486 gauss-seidel spectral radius is 0.9991983 estimated iterations to convergence 279 setup time was (sec) 2.360000 now iterating at: 12:02:39 rms-change max change #iterations 9.277321 343.0997 at 10iterations 5.358346 137.6794 at 20iterations 3.070783 67.22337 at 30iterations 1.755056 43.32812 at 40iterations 0.9977431 22.97343 at 50iterations 0.5646350 13.12284 at 60iterations 0.3196343 7.182178 at 70iterations 0.1806426 3.601704 at 80iterations 0.1018381 1.978445 at 90iterations 5.7293467E-02 1.262089 at 100iterations 3.2235622E-02 0.6695690 at 110iterations 1.8093793E-02 0.3357272 at 120iterations 1.0185950E-02 0.1893358 at 130iterations 5.7211597E-03 0.1107254 at 140iterations 3.2069907E-03 6.3552856E-02 at 150iterations 1.8008710E-03 3.6927223E-02 at 160iterations 1.0112573E-03 1.9287109E-02 at 170iterations 5.6866993E-04 1.1715412E-02 at 180iterations finished qdiffx linear iterations at : 12:02:57 total time elapsed so far: 20.80000 # loops : 180 mean,max change (kT/e) : 5.6866993E-04 1.1715412E-02 energy calculations done at 20.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.02000 DelPhi exited at 12:02:58 21.022u 0.542s 0:21.88 98.5% 0+0k 0+0io 0pf+0w