Sat Oct 8 11:37:59 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+sph2.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 = amb2.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 Sat Oct 8 2011 at 11:37:59 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2866 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: 0.6308142 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): 14.97300 63.29800 ymin,ymax (A): -1.487000 52.91300 zmin,zma (A): -13.11800 43.31700 x,y,z range (A): 48.32500 54.40000 56.43500 scale (grids/A): 0.6308142 object centre (A): 39.13550 25.71300 15.09950 number of atom coordinates read : 2866 total number of charged atoms : 2715 net assigned charge : 8.9108944E-06 assigned positive charge : 423.1393 centred at (gu) : 90.60892 88.06764 90.00620 assigned negative charge : -423.1401 centred at (gu) : 90.59485 88.02538 90.05127 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7793 nv = 96 ne = 84 npr = 56164 no. pairs analyzed = 56164 no. exposed pairs = 4018 no. arc points = 28070 no. surface atoms = 1332 nbur = 1534 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 402 mr = 3917 m= 1 mr = 45 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 0.2000000 number of dielectric boundary points 4234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2717 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9386 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4806940E-09 -4.3724535E-09 midg,1,midg; midg,igrid,midg -6.3020238E-09 2.7634264E-09 1,midg,midg; igrid,midg,midg -1.1388833E-09 1.6744475E-09 gauss-seidel spectral radius is 0.9870181 estimated iterations to convergence 72 setup time was (sec) 0.3800000 now iterating at: 11:37:59 rms-change max change #iterations 0.1400155 18.89070 at 10iterations 1.3590959E-02 1.820451 at 20iterations 1.2991577E-03 0.1873684 at 30iterations 1.2480351E-04 1.8213272E-02 at 40iterations 1.1725274E-05 1.7204285E-03 at 50iterations finished qdiffx linear iterations at : 11:38:02 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.1725274E-05 1.7204285E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 11:38:03 3.357u 0.195s 0:04.23 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 Sat Oct 8 2011 at 11:38:03 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2866 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.892443 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): 14.97300 63.29800 ymin,ymax (A): -1.487000 52.91300 zmin,zma (A): -13.11800 43.31700 x,y,z range (A): 48.32500 54.40000 56.43500 scale (grids/A): 1.892443 object centre (A): 39.13550 25.71300 15.09950 number of atom coordinates read : 2866 total number of charged atoms : 2715 net assigned charge : 8.9108944E-06 assigned positive charge : 423.1393 centred at (gu) : 91.82591 84.20245 90.01805 assigned negative charge : -423.1401 centred at (gu) : 91.78449 84.07563 90.15330 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 83796 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28070 grid for indexing accessible points = 1.400000 m= 28300 mr = 55328 m= 4207 mr = 19548 m= 310 mr = 2467 m= 7 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 186 time to turn everything in is 0.3900000 number of dielectric boundary points 39143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 21327 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) : 0.6308142 object centre at (A) : 39.13550 25.71300 15.09950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2593261E-02 -8.3838785E-03 midg,1,midg; midg,igrid,midg -1.0507572E-02 7.5075729E-03 1,midg,midg; igrid,midg,midg 6.0603847E-03 1.9993799E-02 gauss-seidel spectral radius is 0.9986605 estimated iterations to convergence 216 setup time was (sec) 0.6000000 now iterating at: 11:38:04 rms-change max change #iterations 4.399905 162.5081 at 10iterations 2.082639 67.41620 at 20iterations 0.9798095 29.67019 at 30iterations 0.4591657 14.67510 at 40iterations 0.2172136 7.291794 at 50iterations 0.1020220 2.987140 at 60iterations 4.8147772E-02 1.536354 at 70iterations 2.2640187E-02 0.7016716 at 80iterations 1.0652012E-02 0.3178921 at 90iterations 5.0225048E-03 0.1559715 at 100iterations 2.3785927E-03 7.3781967E-02 at 110iterations 1.1179175E-03 3.3622265E-02 at 120iterations finished qdiffx linear iterations at : 11:38:11 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.1179175E-03 3.3622265E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 11:38:11 7.774u 0.220s 0:08.58 93.1% 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 Sat Oct 8 2011 at 11:38:11 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2866 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: 2.838664 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): 14.97300 63.29800 ymin,ymax (A): -1.487000 52.91300 zmin,zma (A): -13.11800 43.31700 x,y,z range (A): 48.32500 54.40000 56.43500 scale (grids/A): 2.838664 object centre (A): 39.13550 25.71300 15.09950 number of atom coordinates read : 2866 total number of charged atoms : 2715 net assigned charge : 8.9108944E-06 assigned positive charge : 423.1393 centred at (gu) : 92.73888 81.30338 90.02692 assigned negative charge : -423.1401 centred at (gu) : 92.67661 81.11341 90.22992 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 193832 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28070 grid for indexing accessible points = 1.400000 m= 93213 mr = 135282 m= 31563 mr = 73447 m= 7420 mr = 24225 m= 1187 mr = 5309 m= 102 mr = 789 m= 3 mr = 40 m= 0 mr = 2 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 652 time to turn everything in is 1.030000 number of dielectric boundary points 88226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 21718 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) : 1.892443 object centre at (A) : 39.13550 25.71300 15.09950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1804715 0.1229565 midg,1,midg; midg,igrid,midg -9.0896182E-02 5.6470414E-03 1,midg,midg; igrid,midg,midg 5.7585530E-02 0.2703389 gauss-seidel spectral radius is 0.9992844 estimated iterations to convergence 295 setup time was (sec) 1.260000 now iterating at: 11:38:13 rms-change max change #iterations 10.62596 401.0331 at 10iterations 6.388075 135.9313 at 20iterations 3.792519 80.53702 at 30iterations 2.247870 39.76973 at 40iterations 1.322041 29.81892 at 50iterations 0.7762664 15.73057 at 60iterations 0.4545064 8.863983 at 70iterations 0.2654784 5.572632 at 80iterations 0.1549705 2.728519 at 90iterations 9.0311438E-02 1.733421 at 100iterations 5.2718610E-02 0.8880905 at 110iterations 3.0633528E-02 0.6282330 at 120iterations 1.7820137E-02 0.3003297 at 130iterations 1.0342763E-02 0.1822844 at 140iterations 6.0154949E-03 0.1061001 at 150iterations 3.4950331E-03 6.9044113E-02 at 160iterations 2.0289214E-03 3.3367157E-02 at 170iterations 1.1779518E-03 2.1056175E-02 at 180iterations finished qdiffx linear iterations at : 11:38:24 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 1.1779518E-03 2.1056175E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 11:38:25 12.917u 0.221s 0:13.47 97.4% 0+0k 0+0io 0pf+0w