Mon Oct 10 17:03:48 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 17:03:48 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 = 3005 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5404257 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): -31.05100 34.82300 ymin,ymax (A): -25.39300 22.62100 zmin,zma (A): -38.06900 8.148000 x,y,z range (A): 65.87400 48.01400 46.21700 scale (grids/A): 0.5404257 object centre (A): 1.886002 -1.386000 -14.96050 number of atom coordinates read : 3005 total number of charged atoms : 2864 net assigned charge : -1.499979 assigned positive charge : 449.2298 centred at (gu) : 90.43898 90.00764 89.94868 assigned negative charge : -450.7311 centred at (gu) : 90.49178 90.16213 90.03805 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5624 nv = 96 ne = 84 npr = 60391 no. pairs analyzed = 60391 no. exposed pairs = 3868 no. arc points = 26908 no. surface atoms = 1308 nbur = 1697 mkacc time = 9.9999994E-02 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 = 1.596000 m= 229 mr = 2849 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2998 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2749 ## 358 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7450 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1556958E-10 -5.5956201E-10 midg,1,midg; midg,igrid,midg 7.5379047E-10 -9.3587804E-10 1,midg,midg; igrid,midg,midg 1.9098156E-10 -4.0594103E-10 gauss-seidel spectral radius is 0.9823545 estimated iterations to convergence 62 setup time was (sec) 0.4000000 now iterating at: 17:03:48 rms-change max change #iterations 6.8366125E-02 12.75887 at 10iterations 4.5551169E-03 0.8416309 at 20iterations 2.9769778E-04 4.9493790E-02 at 30iterations 2.4401574E-05 4.8999786E-03 at 40iterations 2.9243461E-06 6.9046021E-04 at 50iterations finished qdiffx linear iterations at : 17:03:51 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.9243461E-06 6.9046021E-04 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 17:03:52 3.417u 0.188s 0:04.29 83.6% 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 Mon Oct 10 2011 at 17:03:52 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 = 3005 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.621277 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): -31.05100 34.82300 ymin,ymax (A): -25.39300 22.62100 zmin,zma (A): -38.06900 8.148000 x,y,z range (A): 65.87400 48.01400 46.21700 scale (grids/A): 1.621277 object centre (A): 1.886002 -1.386000 -14.96050 number of atom coordinates read : 3005 total number of charged atoms : 2864 net assigned charge : -1.499979 assigned positive charge : 449.2298 centred at (gu) : 91.31624 90.02239 89.84546 assigned negative charge : -450.7311 centred at (gu) : 91.47497 90.48607 90.11367 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 63080 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26908 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18154 mr = 42313 m= 1586 mr = 12105 m= 34 mr = 663 m= 0 mr = 2 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 607 time to turn everything in is 0.3100000 number of dielectric boundary points 27771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 316 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 21880 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) : 0.5404257 object centre at (A) : 1.886002 -1.386000 -14.96050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1746700E-03 -2.4170666E-03 midg,1,midg; midg,igrid,midg 8.9550624E-03 -1.6314909E-02 1,midg,midg; igrid,midg,midg 9.7406078E-03 -2.5874296E-02 gauss-seidel spectral radius is 0.9981586 estimated iterations to convergence 185 setup time was (sec) 0.5200000 now iterating at: 17:03:53 rms-change max change #iterations 3.260845 153.4943 at 10iterations 1.342629 56.16631 at 20iterations 0.5548466 20.30204 at 30iterations 0.2305882 8.934855 at 40iterations 9.5422655E-02 3.292228 at 50iterations 3.9551929E-02 1.665186 at 60iterations 1.6319312E-02 0.5691940 at 70iterations 6.7720343E-03 0.2499113 at 80iterations 2.8012381E-03 0.1071911 at 90iterations 1.1624803E-03 5.1109314E-02 at 100iterations 4.8338383E-04 1.7389894E-02 at 110iterations 2.0110725E-04 7.5826645E-03 at 120iterations finished qdiffx linear iterations at : 17:04:00 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 2.0110725E-04 7.5826645E-03 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 17:04:01 7.551u 0.189s 0:08.82 87.6% 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 Mon Oct 10 2011 at 17:04:01 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 = 3005 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.431916 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): -31.05100 34.82300 ymin,ymax (A): -25.39300 22.62100 zmin,zma (A): -38.06900 8.148000 x,y,z range (A): 65.87400 48.01400 46.21700 scale (grids/A): 2.431916 object centre (A): 1.886002 -1.386000 -14.96050 number of atom coordinates read : 3005 total number of charged atoms : 2864 net assigned charge : -1.499979 assigned positive charge : 449.2298 centred at (gu) : 91.97413 90.03338 89.76791 assigned negative charge : -450.7311 centred at (gu) : 92.21236 90.72901 90.17033 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 146857 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26908 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 64134 mr = 103972 m= 16822 mr = 49956 m= 2170 mr = 12194 m= 129 mr = 1267 m= 0 mr = 62 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1984 time to turn everything in is 0.7400000 number of dielectric boundary points 62661 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 22875 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) : 1.621277 object centre at (A) : 1.886002 -1.386000 -14.96050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2863360E-02 -2.0933865E-02 midg,1,midg; midg,igrid,midg 0.1519329 -0.2252885 1,midg,midg; igrid,midg,midg 0.6274592 -0.6462142 gauss-seidel spectral radius is 0.9991320 estimated iterations to convergence 268 setup time was (sec) 0.9600000 now iterating at: 17:04:02 rms-change max change #iterations 8.530284 308.1033 at 10iterations 4.758907 120.0454 at 20iterations 2.649675 63.84433 at 30iterations 1.468593 34.48442 at 40iterations 0.8092343 20.56489 at 50iterations 0.4466647 10.01196 at 60iterations 0.2466044 5.995575 at 70iterations 0.1355710 3.089565 at 80iterations 7.4472494E-02 1.838596 at 90iterations 4.0864173E-02 0.9211273 at 100iterations 2.2411438E-02 0.5120296 at 110iterations 1.2288790E-02 0.2780190 at 120iterations 6.7479489E-03 0.1421957 at 130iterations 3.6999702E-03 7.7260971E-02 at 140iterations 2.0297035E-03 4.3025970E-02 at 150iterations 1.1157861E-03 2.2703648E-02 at 160iterations 6.1146176E-04 1.4240265E-02 at 170iterations 3.3604473E-04 6.9031715E-03 at 180iterations finished qdiffx linear iterations at : 17:04:13 total time elapsed so far: 12.04000 # loops : 180 mean,max change (kT/e) : 3.3604473E-04 6.9031715E-03 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.17000 DelPhi exited at 17:04:14 12.175u 0.218s 0:13.40 92.3% 0+0k 0+0io 0pf+0w