Tue Oct 11 03:44:20 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 Tue Oct 11 2011 at 03:44:20 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6360778 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): -11.04400 37.16000 ymin,ymax (A): -26.96700 23.20800 zmin,zma (A): -10.73400 45.23400 x,y,z range (A): 48.20400 50.17500 55.96800 scale (grids/A): 0.6360778 object centre (A): 13.05800 -1.879499 17.25000 number of atom coordinates read : 2781 total number of charged atoms : 2640 net assigned charge : 1.588024 assigned positive charge : 426.7917 centred at (gu) : 89.86533 90.11175 91.94828 assigned negative charge : -425.2042 centred at (gu) : 89.65044 89.98840 91.91371 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7370 nv = 96 ne = 84 npr = 56738 no. pairs analyzed = 56738 no. exposed pairs = 3344 no. arc points = 23205 no. surface atoms = 1125 nbur = 1656 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 360 mr = 4142 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2301 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9038 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2397063E-09 9.1231751E-09 midg,1,midg; midg,igrid,midg -1.1966918E-08 1.6334983E-08 1,midg,midg; igrid,midg,midg -2.3826322E-08 2.5272142E-08 gauss-seidel spectral radius is 0.9872047 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 03:44:20 rms-change max change #iterations 0.1487900 20.73884 at 10iterations 1.4603652E-02 1.958649 at 20iterations 1.4893387E-03 0.2178326 at 30iterations 1.5654757E-04 2.3815155E-02 at 40iterations 1.7816832E-05 2.5367737E-03 at 50iterations finished qdiffx linear iterations at : 03:44:23 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.7816832E-05 2.5367737E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 03:44:24 3.551u 0.195s 0:04.11 90.9% 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 Tue Oct 11 2011 at 03:44:24 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.908233 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): -11.04400 37.16000 ymin,ymax (A): -26.96700 23.20800 zmin,zma (A): -10.73400 45.23400 x,y,z range (A): 48.20400 50.17500 55.96800 scale (grids/A): 1.908233 object centre (A): 13.05800 -1.879499 17.25000 number of atom coordinates read : 2781 total number of charged atoms : 2640 net assigned charge : 1.588024 assigned positive charge : 426.7917 centred at (gu) : 89.59553 90.33469 95.84417 assigned negative charge : -425.2042 centred at (gu) : 88.95123 89.96496 95.74084 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 79778 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23205 grid for indexing accessible points = 1.400000 m= 28629 mr = 56333 m= 4327 mr = 21188 m= 226 mr = 2692 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 404 time to turn everything in is 0.6200000 number of dielectric boundary points 32668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20736 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) : 0.6360778 object centre at (A) : 13.05800 -1.879499 17.25000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2218272E-02 7.9565980E-03 midg,1,midg; midg,igrid,midg -1.8810702E-02 -4.2429417E-03 1,midg,midg; igrid,midg,midg -1.0358419E-02 5.0902255E-02 gauss-seidel spectral radius is 0.9986539 estimated iterations to convergence 216 setup time was (sec) 0.9400000 now iterating at: 03:44:25 rms-change max change #iterations 4.515460 206.6655 at 10iterations 2.128283 84.00029 at 20iterations 1.005766 33.76894 at 30iterations 0.4755422 15.61034 at 40iterations 0.2237449 6.678669 at 50iterations 0.1054532 3.424213 at 60iterations 4.9905032E-02 1.540037 at 70iterations 2.3557827E-02 0.7182522 at 80iterations 1.1117393E-02 0.3289375 at 90iterations 5.2395654E-03 0.1657333 at 100iterations 2.4707811E-03 7.3616028E-02 at 110iterations 1.1724347E-03 3.5077095E-02 at 120iterations finished qdiffx linear iterations at : 03:44:32 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 1.1724347E-03 3.5077095E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 03:44:33 8.073u 0.232s 0:08.70 95.4% 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 Tue Oct 11 2011 at 03:44:33 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.862350 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): -11.04400 37.16000 ymin,ymax (A): -26.96700 23.20800 zmin,zma (A): -10.73400 45.23400 x,y,z range (A): 48.20400 50.17500 55.96800 scale (grids/A): 2.862350 object centre (A): 13.05800 -1.879499 17.25000 number of atom coordinates read : 2781 total number of charged atoms : 2640 net assigned charge : 1.588024 assigned positive charge : 426.7917 centred at (gu) : 89.39327 90.50183 98.76603 assigned negative charge : -425.2042 centred at (gu) : 88.42674 89.94734 98.61115 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 184741 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23205 grid for indexing accessible points = 1.400000 m= 93395 mr = 136513 m= 32754 mr = 76606 m= 7584 mr = 26324 m= 1027 mr = 5735 m= 63 mr = 702 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 1367 time to turn everything in is 1.530000 number of dielectric boundary points 73649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 21102 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) : 1.908233 object centre at (A) : 13.05800 -1.879499 17.25000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5003830 0.2713221 midg,1,midg; midg,igrid,midg -0.2197924 -0.1352036 1,midg,midg; igrid,midg,midg -4.3700777E-02 0.4701545 gauss-seidel spectral radius is 0.9992620 estimated iterations to convergence 290 setup time was (sec) 1.860000 now iterating at: 03:44:35 rms-change max change #iterations 10.48494 420.3677 at 10iterations 6.124111 178.4183 at 20iterations 3.563150 77.83166 at 30iterations 2.060219 40.76439 at 40iterations 1.195958 26.77688 at 50iterations 0.6900283 13.45815 at 60iterations 0.3987505 7.533469 at 70iterations 0.2300124 3.936768 at 80iterations 0.1329036 2.308906 at 90iterations 7.6646402E-02 1.445534 at 100iterations 4.4263653E-02 0.7703662 at 110iterations 2.5475148E-02 0.4461398 at 120iterations 1.4698049E-02 0.2696228 at 130iterations 8.4860474E-03 0.1424942 at 140iterations 4.9031288E-03 8.6248398E-02 at 150iterations 2.8418195E-03 5.2856445E-02 at 160iterations 1.6528091E-03 3.0700684E-02 at 170iterations 9.6810149E-04 1.5991211E-02 at 180iterations finished qdiffx linear iterations at : 03:44:46 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 9.6810149E-04 1.5991211E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 03:44:46 13.112u 0.300s 0:13.74 97.5% 0+0k 0+0io 0pf+0w