Tue Oct 11 01:13:45 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 Tue Oct 11 2011 at 01:13:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2686 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 0.5947110 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): -34.36800 19.51600 ymin,ymax (A): 20.38000 80.24100 zmin,zma (A): 16.91600 60.16400 x,y,z range (A): 53.88400 59.86101 43.24800 scale (grids/A): 0.5947110 object centre (A): -7.426001 50.31050 38.54000 number of atom coordinates read : 2686 total number of charged atoms : 2543 net assigned charge : 5.500015 assigned positive charge : 405.9516 centred at (gu) : 89.10720 87.83667 90.06925 assigned negative charge : -400.4524 centred at (gu) : 89.12691 88.13048 89.91192 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6249 nv = 96 ne = 84 npr = 54156 no. pairs analyzed = 54156 no. exposed pairs = 3153 no. arc points = 22180 no. surface atoms = 1080 nbur = 1606 mkacc time = 0.1800000 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= 272 mr = 3451 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3900000 number of dielectric boundary points 3054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2268 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7858 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2843057E-09 6.7649419E-09 midg,1,midg; midg,igrid,midg 1.7860955E-08 -4.7725344E-09 1,midg,midg; igrid,midg,midg 2.9028326E-09 9.3038094E-10 gauss-seidel spectral radius is 0.9853728 estimated iterations to convergence 68 setup time was (sec) 0.6900000 now iterating at: 01:13:46 rms-change max change #iterations 0.1047148 16.31801 at 10iterations 9.2555704E-03 1.350102 at 20iterations 1.2325812E-03 0.2669411 at 30iterations 2.8978614E-04 7.1235657E-02 at 40iterations 7.9403253E-05 1.9981384E-02 at 50iterations finished qdiffx linear iterations at : 01:13:50 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 7.9403253E-05 1.9981384E-02 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 01:13:51 4.487u 0.374s 0:05.47 88.6% 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 Tue Oct 11 2011 at 01:13:51 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 = 2686 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 1.784133 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): -34.36800 19.51600 ymin,ymax (A): 20.38000 80.24100 zmin,zma (A): 16.91600 60.16400 x,y,z range (A): 53.88400 59.86101 43.24800 scale (grids/A): 1.784133 object centre (A): -7.426001 50.31050 38.54000 number of atom coordinates read : 2686 total number of charged atoms : 2543 net assigned charge : 5.500015 assigned positive charge : 405.9516 centred at (gu) : 87.32063 83.50916 90.20693 assigned negative charge : -400.4524 centred at (gu) : 87.38038 84.39111 89.73547 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 68756 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22180 grid for indexing accessible points = 1.400000 m= 22621 mr = 48327 m= 2919 mr = 16442 m= 117 mr = 1746 m= 0 mr = 23 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 740 time to turn everything in is 0.6800000 number of dielectric boundary points 27875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 19814 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) : 0.5947110 object centre at (A) : -7.426001 50.31050 38.54000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8200918E-03 2.1739887E-02 midg,1,midg; midg,igrid,midg 3.2260250E-02 -2.6359238E-02 1,midg,midg; igrid,midg,midg -1.2614125E-03 -6.4117851E-04 gauss-seidel spectral radius is 0.9984501 estimated iterations to convergence 202 setup time was (sec) 1.000000 now iterating at: 01:13:52 rms-change max change #iterations 3.777777 182.8902 at 10iterations 1.674376 63.14804 at 20iterations 0.7432091 29.39736 at 30iterations 0.3340968 11.10762 at 40iterations 0.1487330 4.586845 at 50iterations 6.6562347E-02 2.162125 at 60iterations 2.9653702E-02 0.9550953 at 70iterations 1.3419406E-02 0.4594622 at 80iterations 6.1128330E-03 0.2347870 at 90iterations 2.8418123E-03 0.1069565 at 100iterations 1.3792122E-03 5.1898956E-02 at 110iterations 7.0172647E-04 3.3027649E-02 at 120iterations finished qdiffx linear iterations at : 01:14:01 total time elapsed so far: 10.05000 # loops : 120 mean,max change (kT/e) : 7.0172647E-04 3.3027649E-02 energy calculations done at 10.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.26000 DelPhi exited at 01:14:02 10.267u 0.470s 0:11.26 95.2% 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 Tue Oct 11 2011 at 01:14:02 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 = 2686 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 2.676199 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): -34.36800 19.51600 ymin,ymax (A): 20.38000 80.24100 zmin,zma (A): 16.91600 60.16400 x,y,z range (A): 53.88400 59.86101 43.24800 scale (grids/A): 2.676199 object centre (A): -7.426001 50.31050 38.54000 number of atom coordinates read : 2686 total number of charged atoms : 2543 net assigned charge : 5.500015 assigned positive charge : 405.9516 centred at (gu) : 85.98054 80.26359 90.31012 assigned negative charge : -400.4524 centred at (gu) : 86.07046 81.58664 89.60312 start vw surface at 0.1600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 159818 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22180 grid for indexing accessible points = 1.400000 m= 76697 mr = 117448 m= 24334 mr = 62792 m= 5025 mr = 19212 m= 498 mr = 3725 m= 26 mr = 296 m= 0 mr = 4 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 2394 time to turn everything in is 1.740000 number of dielectric boundary points 62921 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 20338 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) : 1.784133 object centre at (A) : -7.426001 50.31050 38.54000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0790358E-02 0.2400176 midg,1,midg; midg,igrid,midg 1.9998729E-02 -0.4180087 1,midg,midg; igrid,midg,midg -5.5514134E-02 -8.4792159E-02 gauss-seidel spectral radius is 0.9992037 estimated iterations to convergence 280 setup time was (sec) 2.180000 now iterating at: 01:14:05 rms-change max change #iterations 9.070546 323.6013 at 10iterations 5.148320 108.5126 at 20iterations 2.907351 65.96633 at 30iterations 1.638973 38.59522 at 40iterations 0.9206729 18.97136 at 50iterations 0.5204854 10.53363 at 60iterations 0.2918886 5.564839 at 70iterations 0.1645686 3.286757 at 80iterations 9.2568837E-02 1.796791 at 90iterations 5.2004624E-02 1.053093 at 100iterations 2.9357979E-02 0.5720520 at 110iterations 1.6548095E-02 0.3104439 at 120iterations 9.3746632E-03 0.1886368 at 130iterations 5.3443392E-03 0.1104622 at 140iterations 3.0786663E-03 7.0289612E-02 at 150iterations 1.8113217E-03 3.9443970E-02 at 160iterations 1.1078021E-03 2.7305603E-02 at 170iterations 7.0680643E-04 1.9168854E-02 at 180iterations finished qdiffx linear iterations at : 01:14:20 total time elapsed so far: 17.26000 # loops : 180 mean,max change (kT/e) : 7.0680643E-04 1.9168854E-02 energy calculations done at 17.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.48000 DelPhi exited at 01:14:20 17.484u 0.461s 0:18.37 97.6% 0+0k 0+0io 0pf+0w