Sun Oct 9 01:48:46 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 Sun Oct 9 2011 at 01:48:46 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2311 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6413837 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): -26.93300 26.80600 ymin,ymax (A): 8.193999 51.89700 zmin,zma (A): -11.90200 43.60300 x,y,z range (A): 53.73900 43.70300 55.50500 scale (grids/A): 0.6413837 object centre (A): -6.3500404E-02 30.04550 15.85050 number of atom coordinates read : 2311 total number of charged atoms : 2177 net assigned charge : 10.51402 assigned positive charge : 337.2806 centred at (gu) : 90.66384 90.74643 90.59175 assigned negative charge : -326.7671 centred at (gu) : 90.70286 90.68433 90.62730 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6614 nv = 96 ne = 84 npr = 46035 no. pairs analyzed = 46035 no. exposed pairs = 3134 no. arc points = 22782 no. surface atoms = 1054 nbur = 1257 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 3317 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.1800000 number of dielectric boundary points 3622 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2301 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7768 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7265537E-08 1.3845132E-08 midg,1,midg; midg,igrid,midg 8.2362073E-09 2.5970415E-08 1,midg,midg; igrid,midg,midg 1.7313013E-08 1.3638863E-08 gauss-seidel spectral radius is 0.9873925 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 01:48:47 rms-change max change #iterations 0.1325868 19.72883 at 10iterations 1.3129525E-02 1.881130 at 20iterations 1.2995189E-03 0.1971436 at 30iterations 1.3114755E-04 1.8978119E-02 at 40iterations 1.3100375E-05 1.9531250E-03 at 50iterations finished qdiffx linear iterations at : 01:48:50 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.3100375E-05 1.9531250E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 01:48:50 3.318u 0.537s 0:04.18 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 Sun Oct 9 2011 at 01:48:50 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2311 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.924151 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): -26.93300 26.80600 ymin,ymax (A): 8.193999 51.89700 zmin,zma (A): -11.90200 43.60300 x,y,z range (A): 53.73900 43.70300 55.50500 scale (grids/A): 1.924151 object centre (A): -6.3500404E-02 30.04550 15.85050 number of atom coordinates read : 2311 total number of charged atoms : 2177 net assigned charge : 10.51402 assigned positive charge : 337.2806 centred at (gu) : 91.99124 92.23919 91.77509 assigned negative charge : -326.7671 centred at (gu) : 92.10841 92.05296 91.88204 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 70458 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22782 grid for indexing accessible points = 1.400000 m= 24797 mr = 46396 m= 3965 mr = 17445 m= 264 mr = 2211 m= 5 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 218 time to turn everything in is 0.3400000 number of dielectric boundary points 33380 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 17148 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) : 0.6413837 object centre at (A) : -6.3500404E-02 30.04550 15.85050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1299238E-02 1.7845560E-02 midg,1,midg; midg,igrid,midg -3.0621260E-03 2.5670294E-02 1,midg,midg; igrid,midg,midg 4.2317927E-02 5.0029557E-02 gauss-seidel spectral radius is 0.9986482 estimated iterations to convergence 216 setup time was (sec) 0.5400000 now iterating at: 01:48:51 rms-change max change #iterations 3.949790 165.0706 at 10iterations 1.851222 70.09966 at 20iterations 0.8675596 29.83238 at 30iterations 0.4056512 14.24401 at 40iterations 0.1906297 6.217850 at 50iterations 8.9334466E-02 3.055810 at 60iterations 4.2001307E-02 1.269646 at 70iterations 1.9628808E-02 0.6235857 at 80iterations 9.2247399E-03 0.3071709 at 90iterations 4.3209493E-03 0.1415437 at 100iterations 2.0328255E-03 6.4266205E-02 at 110iterations 9.5234666E-04 2.8911591E-02 at 120iterations finished qdiffx linear iterations at : 01:48:58 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 9.5234666E-04 2.8911591E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 01:48:59 7.699u 0.252s 0:08.27 96.0% 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 Sun Oct 9 2011 at 01:48:59 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2311 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.886227 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): -26.93300 26.80600 ymin,ymax (A): 8.193999 51.89700 zmin,zma (A): -11.90200 43.60300 x,y,z range (A): 53.73900 43.70300 55.50500 scale (grids/A): 2.886227 object centre (A): -6.3500404E-02 30.04550 15.85050 number of atom coordinates read : 2311 total number of charged atoms : 2177 net assigned charge : 10.51402 assigned positive charge : 337.2806 centred at (gu) : 92.98684 93.35870 92.66253 assigned negative charge : -326.7671 centred at (gu) : 93.16270 93.07945 92.82301 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 162566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22782 grid for indexing accessible points = 1.400000 m= 79564 mr = 113009 m= 28774 mr = 63145 m= 7188 mr = 22213 m= 1171 mr = 5033 m= 66 mr = 662 m= 0 mr = 12 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 741 time to turn everything in is 0.9100000 number of dielectric boundary points 75255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 17416 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) : 1.924151 object centre at (A) : -6.3500404E-02 30.04550 15.85050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8967258 0.2284448 midg,1,midg; midg,igrid,midg -5.3430133E-02 0.2367872 1,midg,midg; igrid,midg,midg 0.4224902 0.4897913 gauss-seidel spectral radius is 0.9992735 estimated iterations to convergence 293 setup time was (sec) 1.140000 now iterating at: 01:49:00 rms-change max change #iterations 9.364795 366.2141 at 10iterations 5.520459 123.2183 at 20iterations 3.226718 65.41956 at 30iterations 1.875926 35.52101 at 40iterations 1.092557 22.90382 at 50iterations 0.6317108 12.19300 at 60iterations 0.3666289 7.690864 at 70iterations 0.2127200 4.460144 at 80iterations 0.1228613 2.241563 at 90iterations 7.0945375E-02 1.438985 at 100iterations 4.1005123E-02 0.7313204 at 110iterations 2.3689305E-02 0.5042820 at 120iterations 1.3666650E-02 0.2520227 at 130iterations 7.8896750E-03 0.1462481 at 140iterations 4.5607416E-03 8.9754105E-02 at 150iterations 2.6244537E-03 4.7735214E-02 at 160iterations 1.5154057E-03 2.7488708E-02 at 170iterations 8.7505783E-04 1.6549230E-02 at 180iterations finished qdiffx linear iterations at : 01:49:12 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 8.7505783E-04 1.6549230E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 01:49:12 12.772u 0.216s 0:13.40 96.8% 0+0k 0+0io 0pf+0w