Mon Oct 10 09:18:04 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 09:18:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 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: 0.5819277 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): 112.7790 173.9550 ymin,ymax (A): -45.46100 7.289000 zmin,zma (A): 49.31300 104.0340 x,y,z range (A): 61.17599 52.75000 54.72100 scale (grids/A): 0.5819277 object centre (A): 143.3670 -19.08600 76.67350 number of atom coordinates read : 2857 total number of charged atoms : 2706 net assigned charge : 6.000015 assigned positive charge : 418.3879 centred at (gu) : 89.95654 88.40418 89.06924 assigned negative charge : -412.3884 centred at (gu) : 89.94999 88.50833 88.91680 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6496 nv = 96 ne = 84 npr = 55184 no. pairs analyzed = 55184 no. exposed pairs = 4402 no. arc points = 31923 no. surface atoms = 1455 nbur = 1402 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 = 1.456000 m= 388 mr = 2776 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3147 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8161 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4840470E-09 3.7381165E-09 midg,1,midg; midg,igrid,midg 5.2795865E-09 -5.9459182E-10 1,midg,midg; igrid,midg,midg 1.2650878E-09 1.5216707E-09 gauss-seidel spectral radius is 0.9847677 estimated iterations to convergence 67 setup time was (sec) 0.5200000 now iterating at: 09:18:05 rms-change max change #iterations 9.5849998E-02 17.28607 at 10iterations 7.5532431E-03 1.285084 at 20iterations 5.9040886E-04 0.1048126 at 30iterations 4.5906138E-05 7.3490143E-03 at 40iterations 3.8130897E-06 5.4979324E-04 at 50iterations finished qdiffx linear iterations at : 09:18:07 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 3.8130897E-06 5.4979324E-04 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 09:18:08 3.090u 0.137s 0:03.66 87.9% 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 09:18:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.745783 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): 112.7790 173.9550 ymin,ymax (A): -45.46100 7.289000 zmin,zma (A): 49.31300 104.0340 x,y,z range (A): 61.17599 52.75000 54.72100 scale (grids/A): 1.745783 object centre (A): 143.3670 -19.08600 76.67350 number of atom coordinates read : 2857 total number of charged atoms : 2706 net assigned charge : 6.000015 assigned positive charge : 418.3879 centred at (gu) : 89.86903 85.21230 87.20738 assigned negative charge : -412.3884 centred at (gu) : 89.84981 85.52474 86.75031 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 68241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31923 grid for indexing accessible points = 1.400000 m= 23072 mr = 40632 m= 3684 mr = 14744 m= 192 mr = 1937 m= 0 mr = 18 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 212 time to turn everything in is 0.5300000 number of dielectric boundary points 37858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 248 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 21004 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) : 0.5819277 object centre at (A) : 143.3670 -19.08600 76.67350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1038537E-02 2.9006178E-02 midg,1,midg; midg,igrid,midg 1.5020745E-02 3.2835407E-03 1,midg,midg; igrid,midg,midg 1.5751919E-02 -3.8936030E-04 gauss-seidel spectral radius is 0.9984349 estimated iterations to convergence 201 setup time was (sec) 0.8100000 now iterating at: 09:18:09 rms-change max change #iterations 3.694642 158.6662 at 10iterations 1.634939 59.97065 at 20iterations 0.7245173 26.48956 at 30iterations 0.3198742 12.44810 at 40iterations 0.1411650 4.687078 at 50iterations 6.2333960E-02 2.285179 at 60iterations 2.7654553E-02 0.9707336 at 70iterations 1.2183611E-02 0.4585676 at 80iterations 5.4177288E-03 0.1804619 at 90iterations 2.4011759E-03 8.1420898E-02 at 100iterations 1.0617526E-03 3.4701496E-02 at 110iterations 4.6916155E-04 1.6439915E-02 at 120iterations finished qdiffx linear iterations at : 09:18:15 total time elapsed so far: 7.040000 # loops : 120 mean,max change (kT/e) : 4.6916155E-04 1.6439915E-02 energy calculations done at 7.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.220000 DelPhi exited at 09:18:16 7.222u 0.185s 0:07.68 96.3% 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 09:18:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.618675 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): 112.7790 173.9550 ymin,ymax (A): -45.46100 7.289000 zmin,zma (A): 49.31300 104.0340 x,y,z range (A): 61.17599 52.75000 54.72100 scale (grids/A): 2.618675 object centre (A): 143.3670 -19.08600 76.67350 number of atom coordinates read : 2857 total number of charged atoms : 2706 net assigned charge : 6.000015 assigned positive charge : 418.3879 centred at (gu) : 89.80361 82.81821 85.81083 assigned negative charge : -412.3884 centred at (gu) : 89.77462 83.28705 85.12539 start vw surface at 0.1900000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 157328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31923 grid for indexing accessible points = 1.400000 m= 72050 mr = 100304 m= 26819 mr = 53316 m= 6323 mr = 19764 m= 707 mr = 4180 m= 15 mr = 328 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 761 time to turn everything in is 1.250000 number of dielectric boundary points 85350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 21626 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) : 1.745783 object centre at (A) : 143.3670 -19.08600 76.67350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1666557 0.3966943 midg,1,midg; midg,igrid,midg 0.1173524 9.3239807E-02 1,midg,midg; igrid,midg,midg 0.1681256 -0.1257532 gauss-seidel spectral radius is 0.9992365 estimated iterations to convergence 286 setup time was (sec) 1.540000 now iterating at: 09:18:17 rms-change max change #iterations 9.466645 361.8920 at 10iterations 5.626323 143.2458 at 20iterations 3.285396 75.87292 at 30iterations 1.908683 43.89000 at 40iterations 1.106299 24.75633 at 50iterations 0.6362495 15.23318 at 60iterations 0.3664445 8.514357 at 70iterations 0.2099890 4.354748 at 80iterations 0.1203594 2.429950 at 90iterations 6.8584733E-02 1.535903 at 100iterations 3.9269626E-02 0.8603592 at 110iterations 2.2408890E-02 0.4409733 at 120iterations 1.2758046E-02 0.2579336 at 130iterations 7.2831996E-03 0.1393871 at 140iterations 4.1492162E-03 8.3032608E-02 at 150iterations 2.3631153E-03 4.5780182E-02 at 160iterations 1.3460782E-03 2.6800156E-02 at 170iterations 7.6395314E-04 1.5842915E-02 at 180iterations finished qdiffx linear iterations at : 09:18:28 total time elapsed so far: 11.84000 # loops : 180 mean,max change (kT/e) : 7.6395314E-04 1.5842915E-02 energy calculations done at 11.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.02000 DelPhi exited at 09:18:28 12.023u 0.161s 0:12.48 97.5% 0+0k 0+0io 0pf+0w