Sun Oct 9 06:48:29 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 06:48:29 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6730442 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): -24.57900 26.05500 ymin,ymax (A): 1.401000 46.06700 zmin,zma (A): -23.41800 29.47600 x,y,z range (A): 50.63400 44.66600 52.89400 scale (grids/A): 0.6730442 object centre (A): 0.7379999 23.73400 3.028999 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -2.499986 assigned positive charge : 299.2390 centred at (gu) : 89.24303 89.49585 88.62608 assigned negative charge : -301.7391 centred at (gu) : 89.19618 89.71330 88.57819 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6075 nv = 96 ne = 84 npr = 41911 no. pairs analyzed = 41911 no. exposed pairs = 2465 no. arc points = 17613 no. surface atoms = 836 nbur = 1158 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 3320 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.1600000 number of dielectric boundary points 3044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1657 ## 134 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6971 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5405489E-08 8.1479368E-10 midg,1,midg; midg,igrid,midg 4.0451994E-08 -5.0729803E-08 1,midg,midg; igrid,midg,midg -2.2109957E-08 7.9206508E-10 gauss-seidel spectral radius is 0.9884996 estimated iterations to convergence 76 setup time was (sec) 0.3600000 now iterating at: 06:48:30 rms-change max change #iterations 0.1645308 31.95420 at 10iterations 1.8016499E-02 2.386452 at 20iterations 1.9984911E-03 0.2826328 at 30iterations 2.2182343E-04 3.0345917E-02 at 40iterations 2.4378003E-05 3.2348633E-03 at 50iterations finished qdiffx linear iterations at : 06:48:33 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.4378003E-05 3.2348633E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 06:48:33 3.374u 0.180s 0:03.89 91.2% 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 06:48:33 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.019133 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): -24.57900 26.05500 ymin,ymax (A): 1.401000 46.06700 zmin,zma (A): -23.41800 29.47600 x,y,z range (A): 50.63400 44.66600 52.89400 scale (grids/A): 2.019133 object centre (A): 0.7379999 23.73400 3.028999 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -2.499986 assigned positive charge : 299.2390 centred at (gu) : 87.72907 88.48763 85.87819 assigned negative charge : -301.7391 centred at (gu) : 87.58869 89.13992 85.73460 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 64967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17613 grid for indexing accessible points = 1.400000 m= 23272 mr = 44788 m= 4099 mr = 17189 m= 323 mr = 2682 m= 8 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1057 time to turn everything in is 0.3200000 number of dielectric boundary points 27890 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14699 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) : 0.6730442 object centre at (A) : 0.7379999 23.73400 3.028999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9795292E-02 3.3673242E-02 midg,1,midg; midg,igrid,midg 4.9554206E-02 -3.8444314E-02 1,midg,midg; igrid,midg,midg -4.7177222E-02 -1.3298322E-02 gauss-seidel spectral radius is 0.9987181 estimated iterations to convergence 221 setup time was (sec) 0.5500000 now iterating at: 06:48:34 rms-change max change #iterations 4.188850 206.4920 at 10iterations 2.000083 74.77432 at 20iterations 0.9598739 33.95724 at 30iterations 0.4593572 16.89230 at 40iterations 0.2195913 7.383059 at 50iterations 0.1051651 3.274410 at 60iterations 5.0485954E-02 1.644056 at 70iterations 2.4151886E-02 0.9181213 at 80iterations 1.1589739E-02 0.3728071 at 90iterations 5.5390755E-03 0.1853905 at 100iterations 2.6693260E-03 0.1031706 at 110iterations 1.2756352E-03 4.1370392E-02 at 120iterations finished qdiffx linear iterations at : 06:48:41 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 1.2756352E-03 4.1370392E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 06:48:42 7.925u 0.216s 0:08.41 96.6% 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 06:48:42 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.028699 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): -24.57900 26.05500 ymin,ymax (A): 1.401000 46.06700 zmin,zma (A): -23.41800 29.47600 x,y,z range (A): 50.63400 44.66600 52.89400 scale (grids/A): 3.028699 object centre (A): 0.7379999 23.73400 3.028999 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -2.499986 assigned positive charge : 299.2390 centred at (gu) : 86.59349 87.73130 83.81723 assigned negative charge : -301.7391 centred at (gu) : 86.38297 88.70985 83.60193 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 149869 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17613 grid for indexing accessible points = 1.400000 m= 74927 mr = 107888 m= 27651 mr = 61508 m= 7615 mr = 22372 m= 1358 mr = 5788 m= 94 mr = 907 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 3875 time to turn everything in is 0.8500000 number of dielectric boundary points 63014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 14840 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) : 2.019133 object centre at (A) : 0.7379999 23.73400 3.028999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5647965 0.8781607 midg,1,midg; midg,igrid,midg 0.5503908 -0.4167967 1,midg,midg; igrid,midg,midg -0.4249726 -9.8299034E-02 gauss-seidel spectral radius is 0.9992694 estimated iterations to convergence 292 setup time was (sec) 1.100000 now iterating at: 06:48:43 rms-change max change #iterations 9.484549 418.5649 at 10iterations 5.471807 131.2081 at 20iterations 3.158137 77.44427 at 30iterations 1.820392 40.51585 at 40iterations 1.049512 20.96492 at 50iterations 0.6035439 11.06780 at 60iterations 0.3479575 6.369431 at 70iterations 0.1995074 3.972885 at 80iterations 0.1152290 2.231680 at 90iterations 6.6395089E-02 1.228518 at 100iterations 3.8271729E-02 0.7215576 at 110iterations 2.2007426E-02 0.4184718 at 120iterations 1.2642059E-02 0.2386193 at 130iterations 7.2867894E-03 0.1398315 at 140iterations 4.1856281E-03 7.6031685E-02 at 150iterations 2.4195050E-03 5.1662445E-02 at 160iterations 1.3926259E-03 2.5600433E-02 at 170iterations 8.0233323E-04 1.5792847E-02 at 180iterations finished qdiffx linear iterations at : 06:48:54 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 8.0233323E-04 1.5792847E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 06:48:55 12.591u 0.225s 0:13.10 97.7% 0+0k 0+0io 0pf+0w