Sat Oct 15 12:02:58 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 Sat Oct 15 2011 at 12:02:58 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3313 !!! WARNING: HIT 88 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 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 : 12.01404 assigned positive charge : 488.6455 centred at (gu) : 90.18878 89.36121 90.37576 assigned negative charge : -476.6334 centred at (gu) : 90.09798 89.27119 90.50145 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 0.6400000 number of grid points assigned charge 8906 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1332280E-09 -2.2449023E-10 midg,1,midg; midg,igrid,midg 1.8963134E-10 1.7029796E-09 1,midg,midg; igrid,midg,midg 1.5674961E-10 2.0868189E-09 gauss-seidel spectral radius is 0.9833251 estimated iterations to convergence 64 setup time was (sec) 0.8300000 now iterating at: 12:02:59 rms-change max change #iterations 8.3109550E-02 13.56744 at 10iterations 5.8692517E-03 0.7982597 at 20iterations 4.1688766E-04 6.1717033E-02 at 30iterations 3.4602053E-05 4.7686100E-03 at 40iterations 4.4285389E-06 4.8255920E-04 at 50iterations finished qdiffx linear iterations at : 12:03:04 total time elapsed so far: 5.170000 # loops : 50 mean,max change (kT/e) : 4.4285389E-06 4.8255920E-04 energy calculations done at 5.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.390000 DelPhi exited at 12:03:04 5.393u 0.432s 0:06.21 93.7% 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 12:03:05 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3313 !!! WARNING: HIT 88 has a net charge of 0.5140 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 : 12.01404 assigned positive charge : 488.6455 centred at (gu) : 90.56557 88.08265 91.12637 assigned negative charge : -476.6334 centred at (gu) : 90.29345 87.81326 91.50390 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 = 0.4000000 no. cavity mid-points inaccessible to solvent = 473 time to turn everything in is 0.8000000 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 0.9400000 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 4.2756042E-03 -7.4197249E-03 midg,1,midg; midg,igrid,midg -3.6783849E-03 2.4061609E-02 1,midg,midg; igrid,midg,midg 7.2486685E-03 1.5536862E-02 gauss-seidel spectral radius is 0.9983170 estimated iterations to convergence 194 setup time was (sec) 1.150000 now iterating at: 12:03:06 rms-change max change #iterations 3.632185 206.2725 at 10iterations 1.552503 76.47726 at 20iterations 0.6650612 20.89028 at 30iterations 0.2861021 9.929810 at 40iterations 0.1226932 4.336319 at 50iterations 5.2919116E-02 1.869488 at 60iterations 2.2731639E-02 0.7784538 at 70iterations 9.7647123E-03 0.3443413 at 80iterations 4.2025056E-03 0.1386642 at 90iterations 1.8069186E-03 6.0688972E-02 at 100iterations 7.7874737E-04 2.4444580E-02 at 110iterations 3.3599400E-04 1.2094498E-02 at 120iterations finished qdiffx linear iterations at : 12:03:17 total time elapsed so far: 12.26000 # loops : 120 mean,max change (kT/e) : 3.3599400E-04 1.2094498E-02 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 12:03:18 12.484u 0.509s 0:13.26 97.8% 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 15 2011 at 12:03:18 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3313 !!! WARNING: HIT 88 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 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 : 12.01404 assigned positive charge : 488.6455 centred at (gu) : 90.84809 87.12361 91.68931 assigned negative charge : -476.6334 centred at (gu) : 90.44020 86.71977 92.25582 start vw surface at 0.1900000 fill in re-entrant regions at 0.6300000 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 = 1.200000 no. cavity mid-points inaccessible to solvent = 1655 time to turn everything in is 2.000000 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 2.150000 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 -0.1112613 -4.6138726E-02 midg,1,midg; midg,igrid,midg -0.1850317 0.3676646 1,midg,midg; igrid,midg,midg 0.1283150 0.1627767 gauss-seidel spectral radius is 0.9991983 estimated iterations to convergence 279 setup time was (sec) 2.380000 now iterating at: 12:03:21 rms-change max change #iterations 9.333499 343.0997 at 10iterations 5.388803 137.6781 at 20iterations 3.087665 67.31068 at 30iterations 1.764623 43.95044 at 40iterations 1.002982 22.96068 at 50iterations 0.5675735 13.11995 at 60iterations 0.3212650 7.098866 at 70iterations 0.1815104 3.605434 at 80iterations 0.1023436 1.991352 at 90iterations 5.7560761E-02 1.257924 at 100iterations 3.2389730E-02 0.6689005 at 110iterations 1.8179925E-02 0.3372040 at 120iterations 1.0232465E-02 0.1911163 at 130iterations 5.7473364E-03 0.1096344 at 140iterations 3.2220213E-03 6.4579010E-02 at 150iterations 1.8090681E-03 3.6418438E-02 at 160iterations 1.0158699E-03 1.9275665E-02 at 170iterations 5.7122397E-04 1.2008667E-02 at 180iterations finished qdiffx linear iterations at : 12:03:40 total time elapsed so far: 21.31000 # loops : 180 mean,max change (kT/e) : 5.7122397E-04 1.2008667E-02 energy calculations done at 21.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.53000 DelPhi exited at 12:03:40 21.532u 0.532s 0:22.39 98.5% 0+0k 0+0io 0pf+0w