Sat Oct 8 17:54:10 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 17:54:10 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 = 4626 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: 0.5169084 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): -1.404000 61.89400 ymin,ymax (A): -29.79500 31.35700 zmin,zma (A): -23.92000 44.95100 x,y,z range (A): 63.29800 61.15200 68.87100 scale (grids/A): 0.5169084 object centre (A): 30.24500 0.7810001 10.51550 number of atom coordinates read : 4626 total number of charged atoms : 4472 net assigned charge : -7.999976 assigned positive charge : 699.6021 centred at (gu) : 91.22018 90.98861 91.31081 assigned negative charge : -707.6069 centred at (gu) : 91.26504 90.92533 91.31380 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8122 nv = 96 ne = 84 npr = 90372 no. pairs analyzed = 90372 no. exposed pairs = 6075 no. arc points = 43249 no. surface atoms = 2035 nbur = 2591 mkacc time = 0.1600000 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 = 1.652000 m= 295 mr = 4036 m= 1 mr = 9 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 4373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4313 ## 622 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 10777 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0036000E-10 -2.2277422E-10 midg,1,midg; midg,igrid,midg -2.8066174E-10 8.0489927E-11 1,midg,midg; igrid,midg,midg -1.8886383E-12 -4.1232096E-10 gauss-seidel spectral radius is 0.9808626 estimated iterations to convergence 60 setup time was (sec) 0.5000000 now iterating at: 17:54:11 rms-change max change #iterations 6.8266995E-02 11.87261 at 10iterations 4.1488921E-03 0.6154680 at 20iterations 4.4547548E-04 7.8170776E-02 at 30iterations 1.1338659E-04 2.2618294E-02 at 40iterations 3.3309294E-05 6.7081451E-03 at 50iterations finished qdiffx linear iterations at : 17:54:14 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 3.3309294E-05 6.7081451E-03 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 17:54:15 3.702u 0.193s 0:04.20 92.6% 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 8 2011 at 17:54:15 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 = 4626 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: 1.550725 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): -1.404000 61.89400 ymin,ymax (A): -29.79500 31.35700 zmin,zma (A): -23.92000 44.95100 x,y,z range (A): 63.29800 61.15200 68.87100 scale (grids/A): 1.550725 object centre (A): 30.24500 0.7810001 10.51550 number of atom coordinates read : 4626 total number of charged atoms : 4472 net assigned charge : -7.999976 assigned positive charge : 699.6021 centred at (gu) : 93.65919 92.96442 93.93093 assigned negative charge : -707.6069 centred at (gu) : 93.79482 92.77565 93.94131 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 91025 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43249 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 27104 mr = 60872 m= 2402 mr = 17884 m= 53 mr = 986 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 578 time to turn everything in is 0.4600000 number of dielectric boundary points 40840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 619 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 33728 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) : 0.5169084 object centre at (A) : 30.24500 0.7810001 10.51550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5414223E-03 -2.5918923E-02 midg,1,midg; midg,igrid,midg -1.8396633E-02 -7.5767213E-03 1,midg,midg; igrid,midg,midg 4.7462359E-03 -2.3330692E-03 gauss-seidel spectral radius is 0.9981595 estimated iterations to convergence 185 setup time was (sec) 0.7100000 now iterating at: 17:54:16 rms-change max change #iterations 3.854352 152.1600 at 10iterations 1.594433 56.81944 at 20iterations 0.6580966 20.83822 at 30iterations 0.2729143 8.927391 at 40iterations 0.1130353 3.951343 at 50iterations 4.7018718E-02 1.522772 at 60iterations 1.9565420E-02 0.5973797 at 70iterations 8.1231855E-03 0.2599411 at 80iterations 3.4085365E-03 0.1167202 at 90iterations 1.4322283E-03 4.8720360E-02 at 100iterations 6.1503670E-04 1.9906998E-02 at 110iterations 2.7314204E-04 1.1353731E-02 at 120iterations finished qdiffx linear iterations at : 17:54:23 total time elapsed so far: 8.580000 # loops : 120 mean,max change (kT/e) : 2.7314204E-04 1.1353731E-02 energy calculations done at 8.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.710000 DelPhi exited at 17:54:24 8.711u 0.253s 0:09.24 96.9% 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 17:54:24 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 = 4626 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: 2.326088 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): -1.404000 61.89400 ymin,ymax (A): -29.79500 31.35700 zmin,zma (A): -23.92000 44.95100 x,y,z range (A): 63.29800 61.15200 68.87100 scale (grids/A): 2.326088 object centre (A): 30.24500 0.7810001 10.51550 number of atom coordinates read : 4626 total number of charged atoms : 4472 net assigned charge : -7.999976 assigned positive charge : 699.6021 centred at (gu) : 95.48840 94.44645 95.89603 assigned negative charge : -707.6069 centred at (gu) : 95.69210 94.16339 95.91174 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 211604 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43249 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 95557 mr = 149326 m= 24979 mr = 74295 m= 3491 mr = 17943 m= 199 mr = 2041 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 1995 time to turn everything in is 1.130000 number of dielectric boundary points 92160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 35689 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) : 1.550725 object centre at (A) : 30.24500 0.7810001 10.51550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1639040 -0.3373553 midg,1,midg; midg,igrid,midg -0.4699239 -0.1551810 1,midg,midg; igrid,midg,midg 6.1485842E-02 -6.9181420E-02 gauss-seidel spectral radius is 0.9991780 estimated iterations to convergence 275 setup time was (sec) 1.410000 now iterating at: 17:54:25 rms-change max change #iterations 10.46854 314.4023 at 10iterations 6.092937 157.9700 at 20iterations 3.507430 79.28690 at 30iterations 2.001521 44.61303 at 40iterations 1.140694 29.37650 at 50iterations 0.6462410 16.72786 at 60iterations 0.3640416 7.779282 at 70iterations 0.2054492 4.820518 at 80iterations 0.1155133 2.423512 at 90iterations 6.4989962E-02 1.313692 at 100iterations 3.6425952E-02 0.6759262 at 110iterations 2.0405790E-02 0.3727303 at 120iterations 1.1430824E-02 0.2002687 at 130iterations 6.3880817E-03 0.1190195 at 140iterations 3.5846569E-03 6.6093445E-02 at 150iterations 2.0132831E-03 3.6008835E-02 at 160iterations 1.1322706E-03 2.1198273E-02 at 170iterations 6.4071943E-04 1.1348605E-02 at 180iterations finished qdiffx linear iterations at : 17:54:39 total time elapsed so far: 14.50000 # loops : 180 mean,max change (kT/e) : 6.4071943E-04 1.1348605E-02 energy calculations done at 14.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.64000 DelPhi exited at 17:54:39 14.638u 0.260s 0:15.25 97.6% 0+0k 0+0io 0pf+0w