Sun Oct 9 18:44:57 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 Sun Oct 9 2011 at 18:44:57 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 = 3270 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5073032 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): -8.490000 61.68500 ymin,ymax (A): -13.73500 35.07900 zmin,zma (A): 18.94100 69.64000 x,y,z range (A): 70.17500 48.81400 50.69900 scale (grids/A): 0.5073032 object centre (A): 26.59750 10.67200 44.29050 number of atom coordinates read : 3270 total number of charged atoms : 3124 net assigned charge : 11.00003 assigned positive charge : 501.4377 centred at (gu) : 90.66581 89.87130 89.35983 assigned negative charge : -490.4390 centred at (gu) : 90.72268 89.96082 89.31826 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5273 nv = 96 ne = 84 npr = 65492 no. pairs analyzed = 65492 no. exposed pairs = 4198 no. arc points = 28915 no. surface atoms = 1413 nbur = 1857 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 = 1.680000 m= 193 mr = 2635 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 2829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2875 ## 470 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7164 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3216857E-11 1.6887358E-10 midg,1,midg; midg,igrid,midg 2.8170333E-10 -4.0679803E-12 1,midg,midg; igrid,midg,midg 1.8726774E-10 5.5063142E-11 gauss-seidel spectral radius is 0.9800192 estimated iterations to convergence 58 setup time was (sec) 0.6400000 now iterating at: 18:44:58 rms-change max change #iterations 5.3833749E-02 9.560326 at 10iterations 3.1820084E-03 0.5276375 at 20iterations 4.4044733E-04 7.1413040E-02 at 30iterations 1.9626268E-04 3.2907009E-02 at 40iterations 9.8840042E-05 1.6884327E-02 at 50iterations finished qdiffx linear iterations at : 18:45:01 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 9.8840042E-05 1.6884327E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 18:45:01 3.536u 0.147s 0:03.96 92.6% 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 18:45:01 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 = 3270 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.521909 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): -8.490000 61.68500 ymin,ymax (A): -13.73500 35.07900 zmin,zma (A): 18.94100 69.64000 x,y,z range (A): 70.17500 48.81400 50.69900 scale (grids/A): 1.521909 object centre (A): 26.59750 10.67200 44.29050 number of atom coordinates read : 3270 total number of charged atoms : 3124 net assigned charge : 11.00003 assigned positive charge : 501.4377 centred at (gu) : 91.99649 89.61282 88.07886 assigned negative charge : -490.4390 centred at (gu) : 92.16768 89.88204 87.95439 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 59674 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28915 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 17229 mr = 40346 m= 1426 mr = 11066 m= 29 mr = 494 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 26452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 430 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 23398 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) : 0.5073032 object centre at (A) : 26.59750 10.67200 44.29050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7173719E-03 4.7617001E-03 midg,1,midg; midg,igrid,midg 6.2471754E-03 -1.7928848E-03 1,midg,midg; igrid,midg,midg 2.3737403E-02 -5.3551430E-03 gauss-seidel spectral radius is 0.9979191 estimated iterations to convergence 174 setup time was (sec) 0.7500000 now iterating at: 18:45:02 rms-change max change #iterations 3.019796 152.9174 at 10iterations 1.180682 53.59041 at 20iterations 0.4649727 18.02930 at 30iterations 0.1831186 7.497696 at 40iterations 7.1866684E-02 2.831497 at 50iterations 2.8330542E-02 1.071294 at 60iterations 1.1229717E-02 0.4585714 at 70iterations 4.5118020E-03 0.1695709 at 80iterations 1.9212204E-03 8.0501318E-02 at 90iterations 9.5184654E-04 4.0447235E-02 at 100iterations 5.9293781E-04 2.2311211E-02 at 110iterations 4.2910464E-04 1.5151501E-02 at 120iterations finished qdiffx linear iterations at : 18:45:08 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 4.2910464E-04 1.5151501E-02 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.300000 DelPhi exited at 18:45:09 7.308u 0.176s 0:07.75 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 Sun Oct 9 2011 at 18:45:09 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 = 3270 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: 2.282864 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): -8.490000 61.68500 ymin,ymax (A): -13.73500 35.07900 zmin,zma (A): 18.94100 69.64000 x,y,z range (A): 70.17500 48.81400 50.69900 scale (grids/A): 2.282864 object centre (A): 26.59750 10.67200 44.29050 number of atom coordinates read : 3270 total number of charged atoms : 3124 net assigned charge : 11.00003 assigned positive charge : 501.4377 centred at (gu) : 92.99453 89.41911 87.11816 assigned negative charge : -490.4390 centred at (gu) : 93.25144 89.82295 86.93136 start vw surface at 0.1600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 138809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28915 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 61355 mr = 99215 m= 15446 mr = 46946 m= 1941 mr = 10675 m= 82 mr = 988 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.070000 number of dielectric boundary points 59786 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 24908 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) : 1.521909 object centre at (A) : 26.59750 10.67200 44.29050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1566345 6.9966488E-02 midg,1,midg; midg,igrid,midg 9.3950436E-02 -5.9604049E-02 1,midg,midg; igrid,midg,midg 0.7460856 -0.2153916 gauss-seidel spectral radius is 0.9990555 estimated iterations to convergence 257 setup time was (sec) 1.370000 now iterating at: 18:45:10 rms-change max change #iterations 8.222806 287.9716 at 10iterations 4.538904 122.5822 at 20iterations 2.493936 63.01709 at 30iterations 1.355401 33.36062 at 40iterations 0.7364871 19.01560 at 50iterations 0.3993352 11.42819 at 60iterations 0.2160116 5.772217 at 70iterations 0.1167710 2.729622 at 80iterations 6.2562726E-02 1.442024 at 90iterations 3.3751350E-02 0.8259382 at 100iterations 1.8175669E-02 0.4597964 at 110iterations 9.7651845E-03 0.2501602 at 120iterations 5.2288431E-03 0.1152229 at 130iterations 2.8051515E-03 6.6272736E-02 at 140iterations 1.5050166E-03 3.9266586E-02 at 150iterations 8.0806547E-04 1.9050598E-02 at 160iterations 4.3278461E-04 9.6426010E-03 at 170iterations 2.3235353E-04 6.0377121E-03 at 180iterations finished qdiffx linear iterations at : 18:45:20 total time elapsed so far: 11.42000 # loops : 180 mean,max change (kT/e) : 2.3235353E-04 6.0377121E-03 energy calculations done at 11.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.60000 DelPhi exited at 18:45:21 11.603u 0.179s 0:12.07 97.5% 0+0k 0+0io 0pf+0w