Mon Oct 10 10:28:24 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 Mon Oct 10 2011 at 10:28:24 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2524 !!! WARNING: HIR 537 has a net charge of 0.5140 !!! WARNING: MN9 956 has a net charge of 1.4000 !!! WARNING: MN9 957 has a net charge of 1.4000 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: 0.5909597 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): -30.73300 29.50800 ymin,ymax (A): 40.89000 94.62600 zmin,zma (A): 3.416000 51.53300 x,y,z range (A): 60.24100 53.73600 48.11700 scale (grids/A): 0.5909597 object centre (A): -0.6125002 67.75800 27.47450 number of atom coordinates read : 2524 total number of charged atoms : 2393 net assigned charge : 10.31401 assigned positive charge : 388.4901 centred at (gu) : 87.30383 90.73085 87.61801 assigned negative charge : -378.1768 centred at (gu) : 87.12185 90.54069 87.58868 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6081 nv = 96 ne = 84 npr = 47088 no. pairs analyzed = 47088 no. exposed pairs = 3700 no. arc points = 26234 no. surface atoms = 1224 nbur = 1300 mkacc time = 0.1000000 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 = 1.456000 m= 331 mr = 2887 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2543 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7406 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3950537E-09 2.4327762E-09 midg,1,midg; midg,igrid,midg -1.4521953E-09 9.7603090E-09 1,midg,midg; igrid,midg,midg -3.1062668E-09 4.3751540E-09 gauss-seidel spectral radius is 0.9851906 estimated iterations to convergence 67 setup time was (sec) 0.5400000 now iterating at: 10:28:25 rms-change max change #iterations 0.1008042 17.00248 at 10iterations 8.2361940E-03 1.433294 at 20iterations 7.2763913E-04 0.1327026 at 30iterations 9.3481765E-05 1.6231537E-02 at 40iterations 1.9421595E-05 4.0102005E-03 at 50iterations finished qdiffx linear iterations at : 10:28:28 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.9421595E-05 4.0102005E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 10:28:28 3.408u 0.217s 0:03.93 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 Mon Oct 10 2011 at 10:28:28 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2524 !!! WARNING: HIR 537 has a net charge of 0.5140 !!! WARNING: MN9 956 has a net charge of 1.4000 !!! WARNING: MN9 957 has a net charge of 1.4000 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: 1.772879 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): -30.73300 29.50800 ymin,ymax (A): 40.89000 94.62600 zmin,zma (A): 3.416000 51.53300 x,y,z range (A): 60.24100 53.73600 48.11700 scale (grids/A): 1.772879 object centre (A): -0.6125002 67.75800 27.47450 number of atom coordinates read : 2524 total number of charged atoms : 2393 net assigned charge : 10.31401 assigned positive charge : 388.4901 centred at (gu) : 81.91095 92.19206 82.85337 assigned negative charge : -378.1768 centred at (gu) : 81.36536 91.62207 82.76608 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 65222 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26234 grid for indexing accessible points = 1.400000 m= 22073 mr = 41913 m= 3060 mr = 14682 m= 140 mr = 1549 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 32318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 18608 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) : 0.5909597 object centre at (A) : -0.6125002 67.75800 27.47450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1875771E-02 1.4471970E-03 midg,1,midg; midg,igrid,midg 2.6800544E-03 4.3628961E-02 1,midg,midg; igrid,midg,midg 1.5087281E-02 2.1711634E-02 gauss-seidel spectral radius is 0.9984349 estimated iterations to convergence 201 setup time was (sec) 0.7600000 now iterating at: 10:28:29 rms-change max change #iterations 3.693335 179.5759 at 10iterations 1.628268 62.14574 at 20iterations 0.7247953 30.34624 at 30iterations 0.3199943 11.00857 at 40iterations 0.1412532 5.416988 at 50iterations 6.2566325E-02 2.175659 at 60iterations 2.7701935E-02 0.9985237 at 70iterations 1.2284406E-02 0.4425650 at 80iterations 5.4575871E-03 0.2105622 at 90iterations 2.4151814E-03 8.4470749E-02 at 100iterations 1.0793807E-03 4.2373657E-02 at 110iterations 4.8220041E-04 1.6088486E-02 at 120iterations finished qdiffx linear iterations at : 10:28:37 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 4.8220041E-04 1.6088486E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 10:28:37 8.233u 0.246s 0:08.86 95.5% 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 10:28:37 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2524 !!! WARNING: HIR 537 has a net charge of 0.5140 !!! WARNING: MN9 956 has a net charge of 1.4000 !!! WARNING: MN9 957 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.659318 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): -30.73300 29.50800 ymin,ymax (A): 40.89000 94.62600 zmin,zma (A): 3.416000 51.53300 x,y,z range (A): 60.24100 53.73600 48.11700 scale (grids/A): 2.659318 object centre (A): -0.6125002 67.75800 27.47450 number of atom coordinates read : 2524 total number of charged atoms : 2393 net assigned charge : 10.31401 assigned positive charge : 388.4901 centred at (gu) : 77.86613 93.28799 79.27997 assigned negative charge : -378.1768 centred at (gu) : 77.04807 92.43300 79.14910 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 150757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26234 grid for indexing accessible points = 1.400000 m= 71722 mr = 102906 m= 24256 mr = 55090 m= 5047 mr = 17822 m= 549 mr = 3348 m= 24 mr = 279 m= 0 mr = 6 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 72904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 19134 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) : 1.772879 object centre at (A) : -0.6125002 67.75800 27.47450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2633044 -3.0203544E-02 midg,1,midg; midg,igrid,midg 7.5303800E-02 0.6880777 1,midg,midg; igrid,midg,midg 0.3513079 0.3439407 gauss-seidel spectral radius is 0.9992226 estimated iterations to convergence 283 setup time was (sec) 1.490000 now iterating at: 10:28:39 rms-change max change #iterations 9.367788 376.5941 at 10iterations 5.503464 183.1829 at 20iterations 3.209227 90.78753 at 30iterations 1.853579 43.08581 at 40iterations 1.065205 23.59110 at 50iterations 0.6097199 15.00246 at 60iterations 0.3480396 7.691923 at 70iterations 0.1985407 4.427025 at 80iterations 0.1129392 2.422788 at 90iterations 6.4259015E-02 1.316689 at 100iterations 3.6492921E-02 0.7812233 at 110iterations 2.0709695E-02 0.4293323 at 120iterations 1.1736649E-02 0.2358246 at 130iterations 6.6659623E-03 0.1322365 at 140iterations 3.7695987E-03 8.0385208E-02 at 150iterations 2.1367746E-03 4.5795918E-02 at 160iterations 1.2106027E-03 2.4898529E-02 at 170iterations 6.8546500E-04 1.4450073E-02 at 180iterations finished qdiffx linear iterations at : 10:28:49 total time elapsed so far: 11.70000 # loops : 180 mean,max change (kT/e) : 6.8546500E-04 1.4450073E-02 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.89000 DelPhi exited at 10:28:50 11.897u 0.244s 0:12.45 97.4% 0+0k 0+0io 0pf+0w