Mon Oct 10 16:02:52 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 Mon Oct 10 2011 at 16:02:52 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 = 4778 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: 0.5400075 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): -19.60500 46.32000 ymin,ymax (A): 8.046000 73.08400 zmin,zma (A): 34.72600 94.95200 x,y,z range (A): 65.92500 65.03800 60.22601 scale (grids/A): 0.5400075 object centre (A): 13.35750 40.56500 64.83900 number of atom coordinates read : 4778 total number of charged atoms : 4619 net assigned charge : 4.000019 assigned positive charge : 717.9875 centred at (gu) : 90.36179 91.01218 89.90833 assigned negative charge : -713.9920 centred at (gu) : 90.36665 90.96246 89.90652 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8863 nv = 96 ne = 84 npr = 98309 no. pairs analyzed = 98309 no. exposed pairs = 5829 no. arc points = 38958 no. surface atoms = 1972 nbur = 2806 mkacc time = 0.1700000 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 = 1.596000 m= 353 mr = 4854 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4020 ## 515 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 11871 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8030903E-10 2.0259279E-10 midg,1,midg; midg,igrid,midg -1.7948516E-10 7.9041812E-10 1,midg,midg; igrid,midg,midg 2.1341677E-10 1.6399052E-10 gauss-seidel spectral radius is 0.9824506 estimated iterations to convergence 62 setup time was (sec) 0.5000000 now iterating at: 16:02:53 rms-change max change #iterations 8.9275800E-02 12.43244 at 10iterations 6.6021755E-03 0.9051132 at 20iterations 1.1656552E-03 0.1919365 at 30iterations 4.2967364E-04 6.2705994E-02 at 40iterations 1.8670384E-04 2.2457123E-02 at 50iterations finished qdiffx linear iterations at : 16:02:55 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.8670384E-04 2.2457123E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 16:02:56 3.503u 0.168s 0:04.29 85.3% 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 Mon Oct 10 2011 at 16:02:56 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 = 4778 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: 1.620023 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): -19.60500 46.32000 ymin,ymax (A): 8.046000 73.08400 zmin,zma (A): 34.72600 94.95200 x,y,z range (A): 65.92500 65.03800 60.22601 scale (grids/A): 1.620023 object centre (A): 13.35750 40.56500 64.83900 number of atom coordinates read : 4778 total number of charged atoms : 4619 net assigned charge : 4.000019 assigned positive charge : 717.9875 centred at (gu) : 91.08385 93.03484 89.72321 assigned negative charge : -713.9920 centred at (gu) : 91.09937 92.88687 89.71908 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 99626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38958 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31721 mr = 70855 m= 3408 mr = 21981 m= 100 mr = 1653 m= 0 mr = 7 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 224 time to turn everything in is 0.4800000 number of dielectric boundary points 40359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 448 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 35294 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) : 0.5400075 object centre at (A) : 13.35750 40.56500 64.83900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4786617E-03 1.2854408E-02 midg,1,midg; midg,igrid,midg -8.0450028E-03 -3.1480198E-05 1,midg,midg; igrid,midg,midg -2.7957579E-02 1.0510648E-02 gauss-seidel spectral radius is 0.9983301 estimated iterations to convergence 194 setup time was (sec) 0.7100000 now iterating at: 16:02:57 rms-change max change #iterations 4.287846 146.3219 at 10iterations 1.854886 63.74007 at 20iterations 0.8010976 24.60268 at 30iterations 0.3470512 10.94807 at 40iterations 0.1501967 4.317245 at 50iterations 6.5125659E-02 1.862070 at 60iterations 2.8470438E-02 0.8942947 at 70iterations 1.2477988E-02 0.3924103 at 80iterations 5.6007672E-03 0.1846390 at 90iterations 2.6497110E-03 8.6475313E-02 at 100iterations 1.3930373E-03 4.3188095E-02 at 110iterations 8.4742991E-04 2.3559570E-02 at 120iterations finished qdiffx linear iterations at : 16:03:04 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 8.4742991E-04 2.3559570E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 16:03:05 7.952u 0.193s 0:08.65 94.1% 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 Mon Oct 10 2011 at 16:03:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4778 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: 2.430034 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): -19.60500 46.32000 ymin,ymax (A): 8.046000 73.08400 zmin,zma (A): 34.72600 94.95200 x,y,z range (A): 65.92500 65.03800 60.22601 scale (grids/A): 2.430034 object centre (A): 13.35750 40.56500 64.83900 number of atom coordinates read : 4778 total number of charged atoms : 4619 net assigned charge : 4.000019 assigned positive charge : 717.9875 centred at (gu) : 91.62540 94.55196 89.58442 assigned negative charge : -713.9920 centred at (gu) : 91.64896 94.33020 89.57850 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 232266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38958 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 110425 mr = 173558 m= 31693 mr = 87840 m= 5169 mr = 23688 m= 341 mr = 3374 m= 5 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 803 time to turn everything in is 1.220000 number of dielectric boundary points 91301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 36903 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) : 1.620023 object centre at (A) : 13.35750 40.56500 64.83900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8799367E-02 0.2175324 midg,1,midg; midg,igrid,midg -0.1576179 9.4718998E-03 1,midg,midg; igrid,midg,midg -0.5950134 0.1536194 gauss-seidel spectral radius is 0.9992211 estimated iterations to convergence 283 setup time was (sec) 1.460000 now iterating at: 16:03:07 rms-change max change #iterations 11.13250 377.3737 at 10iterations 6.537164 181.8657 at 20iterations 3.805516 88.14102 at 30iterations 2.207472 50.68922 at 40iterations 1.274454 25.50715 at 50iterations 0.7337535 14.76114 at 60iterations 0.4214222 7.603065 at 70iterations 0.2412791 4.591938 at 80iterations 0.1381551 2.354914 at 90iterations 7.8819312E-02 1.390133 at 100iterations 4.4955164E-02 0.8249698 at 110iterations 2.5741195E-02 0.4655673 at 120iterations 1.4717842E-02 0.2620177 at 130iterations 8.4514292E-03 0.1497955 at 140iterations 4.9101450E-03 9.7301483E-02 at 150iterations 2.8933615E-03 5.2812576E-02 at 160iterations 1.7647956E-03 2.9962063E-02 at 170iterations 1.1393157E-03 1.9736290E-02 at 180iterations finished qdiffx linear iterations at : 16:03:18 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 1.1393157E-03 1.9736290E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.21000 DelPhi exited at 16:03:19 13.209u 0.207s 0:13.83 96.8% 0+0k 0+0io 0pf+0w