Tue Oct 11 03:43:45 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 03:43:45 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 = 2699 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: 0.6737575 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): -10.71200 37.38100 ymin,ymax (A): -26.63900 21.66100 zmin,zma (A): -6.998000 45.84000 x,y,z range (A): 48.09300 48.30000 52.83800 scale (grids/A): 0.6737575 object centre (A): 13.33450 -2.489000 19.42100 number of atom coordinates read : 2699 total number of charged atoms : 2552 net assigned charge : 4.500017 assigned positive charge : 407.0148 centred at (gu) : 89.94512 90.00652 90.95216 assigned negative charge : -402.5154 centred at (gu) : 89.69364 89.82439 90.92921 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8291 nv = 96 ne = 84 npr = 54941 no. pairs analyzed = 54941 no. exposed pairs = 3277 no. arc points = 22540 no. surface atoms = 1091 nbur = 1608 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 519 mr = 4826 m= 4 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3200000 number of dielectric boundary points 3888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2094 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9587 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3024334E-09 2.8129028E-08 midg,1,midg; midg,igrid,midg -3.7137131E-08 6.8459080E-08 1,midg,midg; igrid,midg,midg -5.8891288E-08 8.6584571E-08 gauss-seidel spectral radius is 0.9885865 estimated iterations to convergence 76 setup time was (sec) 0.6100000 now iterating at: 03:43:47 rms-change max change #iterations 0.1861444 23.38350 at 10iterations 2.0776212E-02 2.500520 at 20iterations 2.3461927E-03 0.2797737 at 30iterations 2.6850612E-04 3.2794952E-02 at 40iterations 3.2300850E-05 3.8547516E-03 at 50iterations finished qdiffx linear iterations at : 03:43:51 total time elapsed so far: 4.860000 # loops : 50 mean,max change (kT/e) : 3.2300850E-05 3.8547516E-03 energy calculations done at 4.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.030000 DelPhi exited at 03:43:52 5.033u 0.470s 0:06.06 90.7% 0+0k 0+0io 6pf+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 03:43:52 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 = 2699 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: 2.021272 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): -10.71200 37.38100 ymin,ymax (A): -26.63900 21.66100 zmin,zma (A): -6.998000 45.84000 x,y,z range (A): 48.09300 48.30000 52.83800 scale (grids/A): 2.021272 object centre (A): 13.33450 -2.489000 19.42100 number of atom coordinates read : 2699 total number of charged atoms : 2552 net assigned charge : 4.500017 assigned positive charge : 407.0148 centred at (gu) : 89.83502 90.01893 92.85575 assigned negative charge : -402.5154 centred at (gu) : 89.08067 89.47292 92.78732 start vw surface at 0.1200000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 88453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22540 grid for indexing accessible points = 1.400000 m= 36021 mr = 63140 m= 6855 mr = 27759 m= 531 mr = 4609 m= 7 mr = 281 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 2393 time to turn everything in is 0.7400000 number of dielectric boundary points 36078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20196 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) : 0.6737575 object centre at (A) : 13.33450 -2.489000 19.42100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5051155E-02 4.0065516E-03 midg,1,midg; midg,igrid,midg -1.0640780E-02 5.5394322E-02 1,midg,midg; igrid,midg,midg -1.2387777E-02 8.1352949E-02 gauss-seidel spectral radius is 0.9987895 estimated iterations to convergence 228 setup time was (sec) 1.070000 now iterating at: 03:43:53 rms-change max change #iterations 4.870224 232.8349 at 10iterations 2.392770 93.91104 at 20iterations 1.171453 34.11165 at 30iterations 0.5748647 16.65239 at 40iterations 0.2820124 7.779103 at 50iterations 0.1387708 4.174619 at 60iterations 6.7923777E-02 1.888424 at 70iterations 3.3422869E-02 1.028704 at 80iterations 1.6388481E-02 0.4985790 at 90iterations 8.0364291E-03 0.2273102 at 100iterations 3.9485204E-03 0.1110916 at 110iterations 1.9408255E-03 5.9425354E-02 at 120iterations finished qdiffx linear iterations at : 03:44:04 total time elapsed so far: 12.02000 # loops : 120 mean,max change (kT/e) : 1.9408255E-03 5.9425354E-02 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 03:44:05 12.194u 0.509s 0:13.32 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 03:44:05 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 = 2699 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: 3.031909 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): -10.71200 37.38100 ymin,ymax (A): -26.63900 21.66100 zmin,zma (A): -6.998000 45.84000 x,y,z range (A): 48.09300 48.30000 52.83800 scale (grids/A): 3.031909 object centre (A): 13.33450 -2.489000 19.42100 number of atom coordinates read : 2699 total number of charged atoms : 2552 net assigned charge : 4.500017 assigned positive charge : 407.0148 centred at (gu) : 89.75232 90.02808 94.28375 assigned negative charge : -402.5154 centred at (gu) : 88.62100 89.20940 94.18086 start vw surface at 0.1200000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 203914 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22540 grid for indexing accessible points = 1.400000 m= 112241 mr = 152163 m= 46052 mr = 93923 m= 12780 mr = 38243 m= 2322 mr = 10026 m= 241 mr = 1757 m= 4 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 8700 time to turn everything in is 2.020000 number of dielectric boundary points 81295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.190000 number of grid points assigned charge 20416 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) : 2.021272 object centre at (A) : 13.33450 -2.489000 19.42100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2967697 0.2543530 midg,1,midg; midg,igrid,midg -0.1261688 0.5826181 1,midg,midg; igrid,midg,midg -3.0793218E-02 0.6810950 gauss-seidel spectral radius is 0.9992955 estimated iterations to convergence 297 setup time was (sec) 2.410000 now iterating at: 03:44:08 rms-change max change #iterations 11.03554 470.6692 at 10iterations 6.527997 134.7291 at 20iterations 3.842554 78.44356 at 30iterations 2.260541 41.54032 at 40iterations 1.328133 23.09036 at 50iterations 0.7779292 14.75670 at 60iterations 0.4562327 8.376009 at 70iterations 0.2678196 4.775428 at 80iterations 0.1567655 3.035141 at 90iterations 9.1581173E-02 1.673704 at 100iterations 5.3665478E-02 0.9202757 at 110iterations 3.1320289E-02 0.5004053 at 120iterations 1.8320300E-02 0.2880402 at 130iterations 1.0734671E-02 0.1803594 at 140iterations 6.2899296E-03 0.1076069 at 150iterations 3.6939306E-03 6.0129166E-02 at 160iterations 2.1822643E-03 3.4114838E-02 at 170iterations 1.2926760E-03 2.3212433E-02 at 180iterations finished qdiffx linear iterations at : 03:44:27 total time elapsed so far: 21.10000 # loops : 180 mean,max change (kT/e) : 1.2926760E-03 2.3212433E-02 energy calculations done at 21.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.27000 DelPhi exited at 03:44:27 21.272u 0.543s 0:22.23 98.1% 0+0k 0+0io 0pf+0w