Sat Oct 8 22:06:32 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 Sat Oct 8 2011 at 22:06:32 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2407 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: 0.6449977 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): -26.73700 27.15800 ymin,ymax (A): 8.322000 49.81400 zmin,zma (A): -12.42000 42.77400 x,y,z range (A): 53.89500 41.49200 55.19400 scale (grids/A): 0.6449977 object centre (A): 0.2104998 29.06800 15.17700 number of atom coordinates read : 2407 total number of charged atoms : 2272 net assigned charge : 11.00002 assigned positive charge : 350.7062 centred at (gu) : 90.09951 90.97040 90.81583 assigned negative charge : -339.7070 centred at (gu) : 90.13542 90.91409 90.79829 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6636 nv = 96 ne = 84 npr = 49140 no. pairs analyzed = 49140 no. exposed pairs = 3156 no. arc points = 22319 no. surface atoms = 1062 nbur = 1345 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 346 mr = 3433 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 69 time to turn everything in is 0.1800000 number of dielectric boundary points 3515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2201 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8101 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3821863E-08 2.4157318E-08 midg,1,midg; midg,igrid,midg 9.6978390E-09 3.0495382E-08 1,midg,midg; igrid,midg,midg 2.2073774E-08 1.4434335E-08 gauss-seidel spectral radius is 0.9875314 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 22:06:33 rms-change max change #iterations 0.1434364 19.60149 at 10iterations 1.4566997E-02 2.375866 at 20iterations 1.6922769E-03 0.2398186 at 30iterations 3.5445092E-04 6.3795090E-02 at 40iterations 1.1370418E-04 2.2638321E-02 at 50iterations finished qdiffx linear iterations at : 22:06:36 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 1.1370418E-04 2.2638321E-02 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 22:06:37 3.594u 0.221s 0:04.12 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 Sat Oct 8 2011 at 22:06:37 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2407 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: 1.934993 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): -26.73700 27.15800 ymin,ymax (A): 8.322000 49.81400 zmin,zma (A): -12.42000 42.77400 x,y,z range (A): 53.89500 41.49200 55.19400 scale (grids/A): 1.934993 object centre (A): 0.2104998 29.06800 15.17700 number of atom coordinates read : 2407 total number of charged atoms : 2272 net assigned charge : 11.00002 assigned positive charge : 350.7062 centred at (gu) : 90.29807 92.91065 92.44732 assigned negative charge : -339.7070 centred at (gu) : 90.40633 92.74220 92.39474 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71101 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22319 grid for indexing accessible points = 1.400000 m= 23705 mr = 47381 m= 3620 mr = 16660 m= 231 mr = 2101 m= 1 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2944 time to turn everything in is 0.3700000 number of dielectric boundary points 32450 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 17924 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) : 0.6449977 object centre at (A) : 0.2104998 29.06800 15.17700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2216126E-02 2.4395943E-02 midg,1,midg; midg,igrid,midg 6.0930807E-04 3.2202449E-02 1,midg,midg; igrid,midg,midg 5.1616449E-02 4.5503225E-02 gauss-seidel spectral radius is 0.9986609 estimated iterations to convergence 217 setup time was (sec) 0.5900000 now iterating at: 22:06:37 rms-change max change #iterations 4.085036 182.3746 at 10iterations 1.923195 73.62307 at 20iterations 0.9117267 30.36513 at 30iterations 0.4278124 13.91792 at 40iterations 0.2007100 6.280849 at 50iterations 9.5012307E-02 3.150127 at 60iterations 4.4837132E-02 1.681107 at 70iterations 2.1093171E-02 0.6682320 at 80iterations 1.0013125E-02 0.3306198 at 90iterations 4.7593433E-03 0.1490459 at 100iterations 2.2950075E-03 7.5793266E-02 at 110iterations 1.1307111E-03 3.9616585E-02 at 120iterations finished qdiffx linear iterations at : 22:06:45 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 1.1307111E-03 3.9616585E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.080000 DelPhi exited at 22:06:45 8.080u 0.218s 0:08.57 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 Sat Oct 8 2011 at 22:06:45 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2407 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: 2.902489 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): -26.73700 27.15800 ymin,ymax (A): 8.322000 49.81400 zmin,zma (A): -12.42000 42.77400 x,y,z range (A): 53.89500 41.49200 55.19400 scale (grids/A): 2.902489 object centre (A): 0.2104998 29.06800 15.17700 number of atom coordinates read : 2407 total number of charged atoms : 2272 net assigned charge : 11.00002 assigned positive charge : 350.7062 centred at (gu) : 90.44707 94.36589 93.67085 assigned negative charge : -339.7070 centred at (gu) : 90.60957 94.11321 93.59222 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 164146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22319 grid for indexing accessible points = 1.400000 m= 77947 mr = 115562 m= 26869 mr = 61718 m= 6466 mr = 20795 m= 903 mr = 4559 m= 46 mr = 526 m= 0 mr = 19 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 9232 time to turn everything in is 0.9100000 number of dielectric boundary points 73198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 18172 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) : 1.934993 object centre at (A) : 0.2104998 29.06800 15.17700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5403918 0.2315608 midg,1,midg; midg,igrid,midg -1.9450877E-02 0.3320854 1,midg,midg; igrid,midg,midg 0.5443074 0.5032419 gauss-seidel spectral radius is 0.9992685 estimated iterations to convergence 292 setup time was (sec) 1.170000 now iterating at: 22:06:47 rms-change max change #iterations 9.641128 453.0120 at 10iterations 5.699071 142.2111 at 20iterations 3.344948 78.98437 at 30iterations 1.951735 44.08569 at 40iterations 1.142821 22.59895 at 50iterations 0.6641086 12.58459 at 60iterations 0.3853484 7.560155 at 70iterations 0.2234102 4.264296 at 80iterations 0.1296099 2.470257 at 90iterations 7.5157002E-02 1.520775 at 100iterations 4.3494154E-02 0.9571533 at 110iterations 2.5129734E-02 0.4874115 at 120iterations 1.4551911E-02 0.2607956 at 130iterations 8.4104752E-03 0.1588647 at 140iterations 4.8606899E-03 9.0524673E-02 at 150iterations 2.8111117E-03 5.2497864E-02 at 160iterations 1.6274843E-03 3.0897141E-02 at 170iterations 9.4758446E-04 1.7796516E-02 at 180iterations finished qdiffx linear iterations at : 22:06:58 total time elapsed so far: 13.00000 # loops : 180 mean,max change (kT/e) : 9.4758446E-04 1.7796516E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 22:06:59 13.133u 0.227s 0:13.63 97.9% 0+0k 0+0io 0pf+0w