Mon Oct 10 14:17:02 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 14:17:03 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3032 !!! WARNING: ADP 667 has a net charge of -2.0000 !!! WARNING: MG6 669 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: 0.5699648 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): -16.20200 46.25800 ymin,ymax (A): -48.31200 13.88000 zmin,zma (A): -9.491000 42.58400 x,y,z range (A): 62.46000 62.19200 52.07500 scale (grids/A): 0.5699648 object centre (A): 15.02800 -17.21600 16.54650 number of atom coordinates read : 3032 total number of charged atoms : 2888 net assigned charge : 1.400008 assigned positive charge : 479.7900 centred at (gu) : 88.38940 90.22565 89.46216 assigned negative charge : -478.3910 centred at (gu) : 88.42728 90.12917 89.54868 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6509 nv = 96 ne = 84 npr = 58876 no. pairs analyzed = 58876 no. exposed pairs = 4173 no. arc points = 29446 no. surface atoms = 1397 nbur = 1635 mkacc time = 0.1200000 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 = 1.540000 m= 304 mr = 3203 m= 4 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3053 ## 360 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8398 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8596171E-09 -1.1244800E-09 midg,1,midg; midg,igrid,midg -1.3754266E-09 1.8975668E-09 1,midg,midg; igrid,midg,midg 1.2187279E-09 -3.0296782E-10 gauss-seidel spectral radius is 0.9841260 estimated iterations to convergence 65 setup time was (sec) 0.5700000 now iterating at: 14:17:03 rms-change max change #iterations 9.6328482E-02 15.04657 at 10iterations 7.1461969E-03 1.285390 at 20iterations 5.3188764E-04 8.1489563E-02 at 30iterations 4.2694988E-05 7.2250366E-03 at 40iterations 4.4385220E-06 6.1798096E-04 at 50iterations finished qdiffx linear iterations at : 14:17:06 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 4.4385220E-06 6.1798096E-04 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 14:17:07 3.666u 0.274s 0:04.25 92.4% 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 Mon Oct 10 2011 at 14:17:07 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3032 !!! WARNING: ADP 667 has a net charge of -2.0000 !!! WARNING: MG6 669 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: 1.709894 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): -16.20200 46.25800 ymin,ymax (A): -48.31200 13.88000 zmin,zma (A): -9.491000 42.58400 x,y,z range (A): 62.46000 62.19200 52.07500 scale (grids/A): 1.709894 object centre (A): 15.02800 -17.21600 16.54650 number of atom coordinates read : 3032 total number of charged atoms : 2888 net assigned charge : 1.400008 assigned positive charge : 479.7900 centred at (gu) : 85.16748 90.67620 88.38585 assigned negative charge : -478.3910 centred at (gu) : 85.28155 90.38717 88.64574 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29446 grid for indexing accessible points = 1.400000 m= 22565 mr = 46739 m= 2610 mr = 14980 m= 72 mr = 1216 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 33343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 282 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 22317 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) : 0.5699648 object centre at (A) : 15.02800 -17.21600 16.54650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3647049E-03 -2.0474376E-02 midg,1,midg; midg,igrid,midg -3.4435384E-03 1.5360488E-02 1,midg,midg; igrid,midg,midg 2.2501545E-02 9.2706420E-03 gauss-seidel spectral radius is 0.9983704 estimated iterations to convergence 197 setup time was (sec) 0.8500000 now iterating at: 14:17:08 rms-change max change #iterations 3.869704 158.7915 at 10iterations 1.673317 62.71925 at 20iterations 0.7288255 26.55595 at 30iterations 0.3164618 10.55060 at 40iterations 0.1380201 4.779057 at 50iterations 6.0257588E-02 2.177579 at 60iterations 2.6230665E-02 0.8872910 at 70iterations 1.1498209E-02 0.3859711 at 80iterations 4.9998676E-03 0.1797419 at 90iterations 2.1801877E-03 8.0478668E-02 at 100iterations 9.5424085E-04 3.5327911E-02 at 110iterations 4.1880886E-04 1.5277863E-02 at 120iterations finished qdiffx linear iterations at : 14:17:16 total time elapsed so far: 8.450000 # loops : 120 mean,max change (kT/e) : 4.1880886E-04 1.5277863E-02 energy calculations done at 8.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.620000 DelPhi exited at 14:17:17 8.622u 0.313s 0:09.69 92.1% 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 14:17:17 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3032 !!! WARNING: ADP 667 has a net charge of -2.0000 !!! WARNING: MG6 669 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: 2.564841 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): -16.20200 46.25800 ymin,ymax (A): -48.31200 13.88000 zmin,zma (A): -9.491000 42.58400 x,y,z range (A): 62.46000 62.19200 52.07500 scale (grids/A): 2.564841 object centre (A): 15.02800 -17.21600 16.54650 number of atom coordinates read : 3032 total number of charged atoms : 2888 net assigned charge : 1.400008 assigned positive charge : 479.7900 centred at (gu) : 82.75105 91.01408 87.57865 assigned negative charge : -478.3910 centred at (gu) : 82.92228 90.58058 87.96848 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 164763 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29446 grid for indexing accessible points = 1.400000 m= 76314 mr = 115183 m= 23095 mr = 58678 m= 4095 mr = 16998 m= 294 mr = 2499 m= 11 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.280000 number of dielectric boundary points 75107 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 23089 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) : 1.709894 object centre at (A) : 15.02800 -17.21600 16.54650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5911035E-02 -0.3185175 midg,1,midg; midg,igrid,midg -3.9281204E-02 9.6216328E-02 1,midg,midg; igrid,midg,midg 0.3372995 6.5945208E-02 gauss-seidel spectral radius is 0.9992013 estimated iterations to convergence 279 setup time was (sec) 1.620000 now iterating at: 14:17:19 rms-change max change #iterations 9.794631 299.2549 at 10iterations 5.675482 135.4327 at 20iterations 3.260417 78.24693 at 30iterations 1.859848 39.30870 at 40iterations 1.058981 22.07520 at 50iterations 0.6012828 13.57852 at 60iterations 0.3408722 7.213096 at 70iterations 0.1926123 3.682441 at 80iterations 0.1088289 2.418263 at 90iterations 6.1536320E-02 1.393465 at 100iterations 3.4719329E-02 0.6644077 at 110iterations 1.9504756E-02 0.4030530 at 120iterations 1.1007568E-02 0.2091675 at 130iterations 6.1973673E-03 0.1264343 at 140iterations 3.4857935E-03 6.7167282E-02 at 150iterations 1.9593234E-03 4.1526794E-02 at 160iterations 1.1039320E-03 2.2312164E-02 at 170iterations 6.1965513E-04 1.1404037E-02 at 180iterations finished qdiffx linear iterations at : 14:17:31 total time elapsed so far: 14.07000 # loops : 180 mean,max change (kT/e) : 6.1965513E-04 1.1404037E-02 energy calculations done at 14.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.24000 DelPhi exited at 14:17:32 14.243u 0.328s 0:15.01 97.0% 0+0k 0+0io 0pf+0w