Mon Oct 10 19:05:40 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 19:05:40 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2311 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: 0.6492677 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): -56.37200 -3.614000 ymin,ymax (A): -3.474000 49.14900 zmin,zma (A): -26.85400 27.97700 x,y,z range (A): 52.75800 52.62300 54.83100 scale (grids/A): 0.6492677 object centre (A): -29.99300 22.83750 0.5614996 number of atom coordinates read : 2311 total number of charged atoms : 2176 net assigned charge : 7.5399876E-06 assigned positive charge : 336.4605 centred at (gu) : 89.99172 88.51400 89.22137 assigned negative charge : -336.4611 centred at (gu) : 90.00620 88.48102 89.26171 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6680 nv = 96 ne = 84 npr = 47272 no. pairs analyzed = 47272 no. exposed pairs = 2931 no. arc points = 20290 no. surface atoms = 994 nbur = 1317 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 3638 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3700000 number of dielectric boundary points 3376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1905 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 7770 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1806587E-09 -4.4119410E-09 midg,1,midg; midg,igrid,midg -5.8793721E-09 3.1147012E-09 1,midg,midg; igrid,midg,midg 1.9000432E-09 -1.8463464E-09 gauss-seidel spectral radius is 0.9876860 estimated iterations to convergence 74 setup time was (sec) 0.7200000 now iterating at: 19:05:41 rms-change max change #iterations 0.1439334 24.07262 at 10iterations 1.4423376E-02 2.336931 at 20iterations 1.5436076E-03 0.2191925 at 30iterations 1.7289571E-04 2.6327133E-02 at 40iterations 2.4402232E-05 3.9405823E-03 at 50iterations finished qdiffx linear iterations at : 19:05:45 total time elapsed so far: 4.360000 # loops : 50 mean,max change (kT/e) : 2.4402232E-05 3.9405823E-03 energy calculations done at 4.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 19:05:46 4.592u 0.371s 0:05.34 92.8% 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 19:05:46 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2311 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: 1.947803 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): -56.37200 -3.614000 ymin,ymax (A): -3.474000 49.14900 zmin,zma (A): -26.85400 27.97700 x,y,z range (A): 52.75800 52.62300 54.83100 scale (grids/A): 1.947803 object centre (A): -29.99300 22.83750 0.5614996 number of atom coordinates read : 2311 total number of charged atoms : 2176 net assigned charge : 7.5399876E-06 assigned positive charge : 336.4605 centred at (gu) : 89.97482 85.54169 87.66386 assigned negative charge : -336.4611 centred at (gu) : 90.01873 85.44299 87.78533 start vw surface at 0.1200000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 71819 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20290 grid for indexing accessible points = 1.400000 m= 26147 mr = 49865 m= 4742 mr = 19098 m= 390 mr = 3024 m= 4 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 754 time to turn everything in is 0.7300000 number of dielectric boundary points 30949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 17183 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) : 0.6492677 object centre at (A) : -29.99300 22.83750 0.5614996 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9127178E-02 1.1534579E-02 midg,1,midg; midg,igrid,midg -1.2678012E-03 1.9449338E-02 1,midg,midg; igrid,midg,midg -3.6762558E-02 -1.4033472E-02 gauss-seidel spectral radius is 0.9986664 estimated iterations to convergence 217 setup time was (sec) 1.070000 now iterating at: 19:05:47 rms-change max change #iterations 4.115013 196.1033 at 10iterations 1.942201 67.76289 at 20iterations 0.9145021 30.85599 at 30iterations 0.4328287 14.44568 at 40iterations 0.2042377 6.474092 at 50iterations 9.6486695E-02 3.168190 at 60iterations 4.5679968E-02 1.502526 at 70iterations 2.1538276E-02 0.7415781 at 80iterations 1.0183084E-02 0.3166792 at 90iterations 4.8381654E-03 0.1649170 at 100iterations 2.2921942E-03 8.2652092E-02 at 110iterations 1.0860711E-03 3.2800674E-02 at 120iterations finished qdiffx linear iterations at : 19:05:59 total time elapsed so far: 12.79000 # loops : 120 mean,max change (kT/e) : 1.0860711E-03 3.2800674E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 19:06:00 13.008u 0.450s 0:13.90 96.7% 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 19:06:00 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2311 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: 2.921705 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): -56.37200 -3.614000 ymin,ymax (A): -3.474000 49.14900 zmin,zma (A): -26.85400 27.97700 x,y,z range (A): 52.75800 52.62300 54.83100 scale (grids/A): 2.921705 object centre (A): -29.99300 22.83750 0.5614996 number of atom coordinates read : 2311 total number of charged atoms : 2176 net assigned charge : 7.5399876E-06 assigned positive charge : 336.4605 centred at (gu) : 89.96224 83.31260 86.49565 assigned negative charge : -336.4611 centred at (gu) : 90.02821 83.16454 86.67794 start vw surface at 0.1500000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 166364 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20290 grid for indexing accessible points = 1.400000 m= 83535 mr = 120951 m= 31810 mr = 68234 m= 8700 mr = 25385 m= 1650 mr = 6568 m= 160 mr = 1136 m= 6 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 2544 time to turn everything in is 2.040000 number of dielectric boundary points 69848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 17407 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) : 1.947803 object centre at (A) : -29.99300 22.83750 0.5614996 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6311761 0.1227550 midg,1,midg; midg,igrid,midg 0.3042709 0.1714467 1,midg,midg; igrid,midg,midg -0.4021396 -0.2213953 gauss-seidel spectral radius is 0.9992639 estimated iterations to convergence 291 setup time was (sec) 2.370000 now iterating at: 19:06:02 rms-change max change #iterations 9.666361 385.3574 at 10iterations 5.724565 162.1689 at 20iterations 3.380637 77.96446 at 30iterations 1.983919 49.48790 at 40iterations 1.157477 22.40895 at 50iterations 0.6748484 12.83662 at 60iterations 0.3921885 8.564919 at 70iterations 0.2272010 4.122570 at 80iterations 0.1316321 2.681792 at 90iterations 7.6406822E-02 1.583270 at 100iterations 4.4180714E-02 0.8445024 at 110iterations 2.5467388E-02 0.4469481 at 120iterations 1.4741343E-02 0.2719021 at 130iterations 8.5180067E-03 0.1598611 at 140iterations 4.9366853E-03 9.5330238E-02 at 150iterations 2.8711460E-03 5.2690506E-02 at 160iterations 1.6817751E-03 3.6382675E-02 at 170iterations 9.9889678E-04 2.1228790E-02 at 180iterations finished qdiffx linear iterations at : 19:06:18 total time elapsed so far: 18.02000 # loops : 180 mean,max change (kT/e) : 9.9889678E-04 2.1228790E-02 energy calculations done at 18.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.24000 DelPhi exited at 19:06:19 18.243u 0.485s 0:19.06 98.2% 0+0k 0+0io 0pf+0w